diff --git a/.gitignore b/.gitignore
index e6966e87db118e219ac28c2aeaa064003245a426..73051c90863e872cd39cdaa7dc3c86cbd0e47c3e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@ nextflow
 .nextflow.log*
 .nextflow/
 work/
+results
diff --git a/.gitmodules b/.gitmodules
index b271cfbeb43a4c0d1df411f0a4770b047a3cd102..57a4299ee7c8cceac71f9f7c3150d8f9a0b771e9 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "src/sge_modules"]
-	path = src/sge_modules
+	path = src/psmn_modules
 	url = gitlab_lbmc:PSMN/modules.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 43ec4e433b23a3fbfd4ec2b2f6e1cb3ac2a28e2b..afb1991f3308f56efbde1721558a6cb6630ef366 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [0.2.9] - 2019-03-26
+### Added
+- Add new tools (fastq, macs2, umitools, ...)
+- singularity support
+
+### Changed
+- every tool name is now in lowercase in each module section
+
+## [0.2.7] - 2018-10-23
+### Added
+- Add new tools (BWA, GATK, sambamba, ...)
+
+### Changed
+- `sge` profile is now called `psmn` profile to prepare tests in the CCIN2P3
+- every `psmn` config file has an update configuration for mono or 16 cpus queues
+- update process naming to follow new nextflow format
+
 ## [0.2.6] - 2018-08-23
 ### Added
 - Added `src/training_dataset.nf` to build a small training dataset from NGS data
@@ -78,4 +96,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [0.1.0] - 2018-05-06
 This is the first working version of the repository as a nextflow module repository
-
diff --git a/README.md b/README.md
index 2322dbb488ec7be4ec0407a8fec6c99a0fd7f9d6..1df7bd0fe213250e36d01ffad7687ac444821827 100644
--- a/README.md
+++ b/README.md
@@ -73,35 +73,44 @@ src/nf_modules/<tool_name>/<tool_version>/tests.sh
 For example to run the tests on `Bowtie2` run:
 
 ```sh
-src/nf_modules/Bowtie2/tests.sh
+src/nf_modules/bowtie2/tests.sh
 ```
 
 ## Available tools
 
-| tool | nf module | docker module | sge module |
+| tool | nf module | docker module | psmn module |
 |------|:---------:|:-------------:|:----------:|
 BEDtools | ok | ok | ok
+BFCtools |**no**  | ok | ok
+bioawk |**no**  | ok | ok
 Bowtie | ok | ok | **no**
 Bowtie2 | ok | ok | ok
+BWA | ok | ok | ok
 canu | ok | ok | ok
 cutadapt | ok | ok | ok
-deepTools | **no** | ok | ok
+deepTools | ok | ok | ok
+fastp | ok | ok | ok
 FastQC | ok | ok | ok
 file_handle | **no** | ok | ok
+GATK | **no** | ok | ok
 HISAT2 | **no** | ok | **no**
 HTSeq | ok | ok | ok
 Kallisto | ok | ok | ok
-MACS2 | **no** | ok | ok
+MACS2 | ok | ok | ok
 MultiQC | ok | ok | ok
 MUSIC | ok | ok | ok
 picard | **no** | ok | ok
 pigz | **no** | ok | ok
 RSEM | ok | ok | ok
+Salmon | **no** | ok | ok
+sambamba | ok | ok | ok
+samblaster | ok | ok | ok
 SAMtools | ok | ok | ok
 SRAtoolkit | ok | ok | ok
-Salmon | **no** | ok | ok
+subread | **no** | ok | ok
 TopHat | **no** | ok | ok
 Trimmomatic | **no** | ok | ok
+UMItools  | **no** | ok | ok
 UrQt | ok | ok | ok
 
 
@@ -111,7 +120,7 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 ## Versioning
 
-We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags). 
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags).
 
 ## Authors
 
@@ -122,4 +131,3 @@ See also the list of [contributors](https://gitlab.biologie.ens-lyon.fr/pipeline
 ## License
 
 This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details
-
diff --git a/bin/.gitignore b/bin/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..72e8ffc0db8aad71a934dd11e5968bd5109e54b4
--- /dev/null
+++ b/bin/.gitignore
@@ -0,0 +1 @@
+*
diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md
index 09b9574e5bb2171799e987225389ab4cb39f891b..695a16ec3855102584ce48b1c63787213bae99d9 100644
--- a/doc/TP_computational_biologists.md
+++ b/doc/TP_computational_biologists.md
@@ -21,26 +21,26 @@ For the practical you can either work with the WebIDE of Gitlab, or locally as d
 
 To run a tool within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`.
 
-[`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:
+[`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:
 
 ```sh
-$ ls -l src/docker_modules/Kallisto/0.43.1/
-total 16K                                                                        
-drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./                                  
-drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../                                 
--rw-r--r-- 1 laurent users  587 Jun  5 19:06 Dockerfile                          
--rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*                     
+$ ls -l src/docker_modules/kallisto/0.43.1/
+total 16K
+drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./
+drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../
+-rw-r--r-- 1 laurent users  587 Jun  5 19:06 Dockerfile
+-rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*
 ```
 
-## [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh)
-The [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.
+## [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh)
+The [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.
 
 Remember that the name of the [container](https://www.docker.com/what-container) must be in lower case and in the format `<tool_name>:<version>`.
 For tools without a version number you can use a commit hash instead.
 
-## [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile)
+## [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile)
 
-The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) file.
+The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) file.
 
 For `Kallisto` version `0.44.0` the header of the `Dockerfile` is :
 
@@ -57,12 +57,12 @@ Then we declare the *maintainer* of the container. Before declaring an environme
 
 You should always declare a variable `TOOLSNAME_VERSION` that contains the version number of commit number of the tools you wrap. In simple cases you just have to modify this line to create a new `Dockerfile` for another version of the tool.
 
-The following lines of the [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
+The following lines of the [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
 Each `RUN` block is run sequentially by `Docker`. If there is an error or modifications in a `RUN` block, only this block and the following `RUN` will be executed.
 
 You can learn more about the building of Docker containers [here](https://docs.docker.com/engine/reference/builder/#usage).
 
-When you build your [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.
+When you build your [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.
 
 ```sh
 docker run -it ubuntu:18.04 bash
@@ -80,29 +80,23 @@ You can read the Contributing guide for the [PMSN/modules](https://gitlab.biolog
 The last step to wrap your tool is to make it available in nextflow. For this you need to create at least 4 files, like the following for Kallisto version `0.44.0`:
 
 ```sh
-ls -lR src/nf_modules/Kallisto
-src/nf_modules/Kallisto/:
+ls -lR src/nf_modules/kallisto
+src/nf_modules/kallisto/:
 total 12
--rw-r--r-- 1 laurent users 866 Jun 18 17:13 kallisto.config
--rw-r--r-- 1 laurent users 2711 Jun 18 17:13 kallisto.nf
-drwxr-xr-x 2 laurent users 4096 Jun 18 17:14 tests/
-
-src/nf_modules/Kallisto/tests:
-total 16
 -rw-r--r-- 1 laurent users 551 Jun 18 17:14 index.nf
 -rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf
 -rw-r--r-- 1 laurent users 1037 Jun 18 17:14 mapping_single.nf
 -rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
 ```
 
-The [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config) file contains instructions for two profiles : `sge` and `docker`.
-The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains nextflow processes to use `Kallisto`.
+The [`.config` files](./src/nf_modules/kallisto/) file contains instructions for two profiles : `psmn` and `docker`.
+The [`.nf` files](./src/nf_modules/kallisto/) file contains nextflow processes to use `Kallisto`.
 
-The [`tests/tests.sh`](./src/nf_modules/Kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the [`tests/`](./src/nf_modules/kallisto/tests/) folder. Those tests correspond to execution of the processes present in the [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
+The [`tests/tests.sh`](./src/nf_modules/kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the folder. Those tests correspond to execution of the `*.nf` files present in the [`kallisto folder`](./src/nf_modules/kallisto/) on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
 
-## [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config)
+## [`kallisto.config`](./src/nf_modules/kallisto/)
 
-The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `sge` and `docker` profile.
+The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `psmn` and `docker` profile.
 
 ```Groovy
 profiles {
@@ -112,7 +106,7 @@ profiles {
     process {
     }
   }
-  sge {
+  psmn {
     process{
     }
   }
@@ -125,52 +119,50 @@ For example, for `Kallisto` with the version `0.44.0`, we have:
 
 ```Groovy
 process {
-  $index_fasta {
+  withName: index_fasta {
     container = "kallisto:0.44.0"
   }
-  $mapping_fastq {
+  withName: mapping_fastq {
     container = "kallisto:0.44.0"
   }
 }
 ```
 
-### `sge` profile
+### `psmn` profile
 
-The `sge` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
+The `psmn` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
 For example, for `Kallisto`, we have:
 
 ```Groovy
 process{
-  $index_fasta {
-    beforeScript = "module purge; module load Kallisto/0.44.0"
+  withName: index_fasta {
+    beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+    module = "Kallisto/0.44.0"
     executor = "sge"
-    cpus = 1
-    memory = "5GB"
-    time = "6h"
-    queueSize = 1000
-    pollInterval = '60sec'
-    queue = 'h6-E5-2667v4deb128'
-    penv = 'openmp8'
+    cpus = 16
+    memory = "30GB"
+    time = "24h"
+    queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+    penv = 'openmp16'
   }
-  $mapping_fastq {
-    beforeScript = "module purge; module load Kallisto/0.44.0"
+  withName: mapping_fastq {
+    beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+    module = "Kallisto/0.44.0"
     executor = "sge"
-    cpus = 4
-    memory = "5GB"
-    time = "6h"
-    queueSize = 1000
-    pollInterval = '60sec'
-    queue = 'h6-E5-2667v4deb128'
-    penv = 'openmp8'
+    cpus = 16
+    memory = "30GB"
+    time = "24h"
+    queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+    penv = 'openmp16'
   }
 }
 ```
 
 The `beforeScript` variable is executed before the main script for the corresponding process.
 
-## [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf)
+## [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf)
 
-The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.
+The [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.
 
 - Each example must be usable as it is to be incorporated in a nextflow pipeline.
 - You need to define, default value for the parameters passed to the process. 
diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 8fddce8553c6770862dfe24a6da7dd968123dfe8..1a2f3857c24702c4fa4430a97d51658f834fdea8 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -42,15 +42,16 @@ You are now on the main page of your fork of the [pipelines/nextflow](https://gi
 
 The [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file contains instructions to run your pipeline and test its installation.
 
-The [CONTRIBUTING.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md) file contains guidelines to follow if you want to contribute to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) (making a merge request for example).
+The [CONTRIBUTING.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md) file contains guidelines if you want to contribute to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) (making a merge request for example).
 
 The [data](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/data) folder will be the place where you store the raw data for your analysis.
 The [results](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/results) folder will be the place where you store the results of your analysis.
-Note that the content of these two folders should never be saved on git.
+
+> **The content of `data` and `results` folders should never be saved on git.**
 
 The [doc](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc) folder contains the documentation of this practical course.
 
-And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrap tools. This folder contains two subdirectories. A `docker_modules`, a `nf_modules` and a `sge_modules` folder. 
+And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrap tools. This folder contains two subdirectories. A `docker_modules`, a `nf_modules` and a `psmn_modules` folder. 
 
 ### `docker_modules`
 
@@ -58,16 +59,16 @@ The `src/docker_modules` contains the code to wrap tools in [Docker](https://www
 
 ```sh
 ls -l src/docker_modules/
-rwxr-xr-x  3 laurent _lpoperator   96 May 25 15:42 BEDtools/
-drwxr-xr-x  4 laurent _lpoperator  128 Jun 5 16:14 Bowtie2/
-drwxr-xr-x  3 laurent _lpoperator   96 May 25 15:42 FastQC/
-drwxr-xr-x  4 laurent _lpoperator  128 Jun 5 16:14 HTSeq/
+rwxr-xr-x  3 laurent _lpoperator   96 May 25 15:42 bedtools/
+drwxr-xr-x  4 laurent _lpoperator  128 Jun 5 16:14 bowtie2/
+drwxr-xr-x  3 laurent _lpoperator   96 May 25 15:42 fastqc/
+drwxr-xr-x  4 laurent _lpoperator  128 Jun 5 16:14 htseq/
 ```
 
 To each `tools/version` corresponds two files:
 
 ```sh
-ls -l src/docker_modules/Bowtie2/2.3.4.1/
+ls -l src/docker_modules/bowtie2/2.3.4.1/
 -rw-r--r-- 1 laurent _lpoperator  283 Jun  5 15:07 Dockerfile
 -rwxr-xr-x  1 laurent _lpoperator   79 Jun 5 16:18 docker_init.sh*
 ```
@@ -81,9 +82,9 @@ By running this script you will be able to easily install tools in different ver
 - You don’t have to bother with tedious installation procedures, somebody else already did the job and wrote a `Dockerfile`.
 - You can easily keep [containers](https://www.docker.com/what-container) for different version of the same tools.
 
-### `sge_modules`
+### `psmn_modules`
 
-The `src/sge_modules` folder is not really there. It’s a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command:
+The `src/psmn_modules` folder is not really there. It’s a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command:
 
 ```sh
 git submodule init
@@ -94,7 +95,7 @@ The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/REA
 
 ### `nf_modules`
 
-The `src/nf_modules` folder contains templates of [nextflow](https://www.nextflow.io/) wrappers for the tools available in [Docker](https://www.docker.com/what-docker) and [SGE](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:sge). The details of the [nextflow](https://www.nextflow.io/) wrapper will be presented in the next section. Alongside the `.nf` and `.config` there is a `tests` folder that contains a `tests.sh` script to run test on the tool.
+The `src/nf_modules` folder contains templates of [nextflow](https://www.nextflow.io/) wrappers for the tools available in [Docker](https://www.docker.com/what-docker) and [psmn](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:psmn). The details of the [nextflow](https://www.nextflow.io/) wrapper will be presented in the next section. Alongside the `.nf` and `.config` files, there is a `tests.sh` script to run test on the tool.
 
 # Nextflow pipeline
 
@@ -119,14 +120,14 @@ head ${fasta} > sample.fasta
 }
 ```
 
-We have the process `sample_fasta` that takes as `fasta_file` channel as input and output a `fasta_sample` channel. The process itself is defined in the `script:` block and within `"""`.
+We have the process `sample_fasta` that takes a `fasta_file` **channel** as input and as output a `fasta_sample` **channel**. The process itself is defined in the `script:` block and within `"""`.
 
 ```Groovy
 input:
 file fasta from fasta_file
 ```
 
-When we zoom on the `input:` block we see that we define a variable `fasta` of type `file` from the `fasta_file` channel. This mean that groovy is going to write a file named as the content of the variable `fasta` in the root of the folder where `script:` is executed.
+When we zoom on the `input:` block we see that we define a variable `fasta` of type `file` from the `fasta_file` **channel**. This mean that groovy is going to write a file named as the content of the variable `fasta` in the root of the folder where `script:` is executed.
 
 
 ```Groovy
@@ -134,9 +135,9 @@ output:
 file "sample.fasta" into fasta_sample
 ```
 
-At the end of the script, a file named `sample.fasta` is found in the root the folder where `script:` is executed and send into the pipeline `fasta_sample`
+At the end of the script, a file named `sample.fasta` is found in the root the folder where `script:` is executed and send into the **channel** `fasta_sample`.
 
-Using the WebIDE of Gitlab, create a file `src/fasta_sampler.nf` with this process and commit to your repository.
+Using the WebIDE of Gitlab, create a file `src/fasta_sampler.nf` with this process and commit it to your repository.
 
 ![webide](img/webide.png)
 
@@ -144,7 +145,7 @@ Using the WebIDE of Gitlab, create a file `src/fasta_sampler.nf` with this proce
 
 Why bother with channels? In the above example, the advantages of channels are not really clear. We could have just given the `fasta` file to the process. But what if we have many fasta files to process? What if we have sub processes to run on each of the sampled fasta files? Nextflow can easily deal with these problems with the help of channels.
 
-Channels are streams of items that are emitted by a source and consumed by a process. A process with a channel as input will be run on every item send through the channel.
+> **Channels** are streams of items that are emitted by a source and consumed by a process. A process with a channel as input will be run on every item send through the channel.
 
 ```Groovy
 Channel
@@ -152,9 +153,9 @@ Channel
   .set { fasta_file }
 ```
 
-Here we defined the channel `fasta_file` that is going to send every fasta file from the folder `data/fasta/` into the process that take it as input.
+Here we defined the channel `fasta_file` that is going to send every fasta file from the folder `data/tiny_dataset/fasta/` into the process that take it as input.
 
-Add the definition of the channel to the `src/fasta_sampler.nf` file and commit to your repository.
+Add the definition of the channel to the `src/fasta_sampler.nf` file and commit it to your repository.
 
 
 ## Run your pipeline locally
@@ -163,8 +164,20 @@ After writing this first pipeline, you may want to test it. To do that, first cl
 
 You can then run the following commands to download your project on your computer:
 
+If you are on a PSMN computer:
+
+```sh
+pip install cutadapt=1.14
+PATH="/scratch/lmodolo/:$PATH"
+git config --global http.sslVerify false
+```
+
+and then :
+
+> Don't forget to replace *https://gitlab.biologie.ens-lyon.fr/* by *gitlab_lbmc* if you are using your own computer
+
 ```sh
-git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
+git clone https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
 cd nextflow
 src/install_nextflow.sh
 ```
@@ -173,7 +186,7 @@ We also need data to run our pipeline:
 
 ```
 cd data
-git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
 cd ..
 ```
 
@@ -206,7 +219,7 @@ You can run your pipeline again and check the content of the folder `results/sam
 
 ## Fasta everywhere
 
-We ran our pipeline on one fasta file. How nextflow would handle 100 of them? To test that we need to duplicate the `tiny_v2.fasta` file: 
+We ran our pipeline on one fasta file. How would nextflow handle 100 of them? To test that we need to duplicate the `tiny_v2.fasta` file: 
 
 ```sh
 for i in {1..100}
@@ -229,7 +242,7 @@ head ${fasta} > ${fasta.baseName}_sample.fasta
 """
 ```
 
-Add this to your `src/fasta_sampler.nf` file with the WebIDE and commit to your repository before pulling your modifications locally.
+Add this to your `src/fasta_sampler.nf` file with the WebIDE and commit it to your repository before pulling your modifications locally.
 You can run your pipeline again and check the content of the folder `results/sampling`.
 
 # Build your own RNASeq pipeline
@@ -246,7 +259,7 @@ For this practical, we are going to need the following tools:
 
 To initialize these tools, follow the **Installing** section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file.
 
-If you are using a CBP computer don’t forget to clean up your docker containers at the end of the practical with the following command:
+**If you are using a CBP computer don’t forget to clean up your docker containers at the end of the practical with the following commands:**
 
 ```sh
 docker rm $(docker stop $(docker ps -aq))
@@ -255,9 +268,9 @@ docker rmi $(docker images -qf "dangling=true")
 
 ## Cutadapt
 
-The first step of the pipeline is to remove any Illumina adaptor left in your read files.
+The first step of the pipeline is to remove any Illumina adaptors left in your read files.
 
-Open the WebIDE and create a `src/RNASeq.nf` file. Browse for [src/nf_modules/cutadapt/cutadapt.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/cutadapt.nf), this file contains examples for cutadapt. We are interested in the *Illumina adaptor removal*, *for paired-end data* section of the code. Copy this code in your pipeline and commit.
+Open the WebIDE and create a `src/RNASeq.nf` file. Browse for [src/nf_modules/cutadapt/adaptor_removal_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.nf), this file contains examples for cutadapt. We are interested in the *Illumina adaptor removal*, *for paired-end data* section of the code. Copy this code in your pipeline and commit it.
 
 Compared to before, we have few new lines:
 
@@ -265,7 +278,8 @@ Compared to before, we have few new lines:
 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 ```
 
-We declare a variable that contain the path of the fastq file to look for. The advantage of using `params.fastq` is that now the option `--fastq` in our call to the pipeline allows us to define this variable:
+We declare a variable that contains the path of the fastq file to look for. The advantage of using `params.fastq` is that the option `--fastq` is now a parameter of your pipeline.
+Thus, you can call your pipeline with the `--fastq` option:
 
 ```sh
 ./nextflow src/RNASeq.nf --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq"
@@ -291,11 +305,11 @@ For the `fastq_sampler.nf` pipeline we used the command `head` present in most b
 
 - install cutadapt locally so nextflow can use it
 - launch the process in a Docker container that has cutadapt installed
-- launch the process with SGE while loading the correct module to have cutadapt available
+- launch the process with psmn while loading the correct module to have cutadapt available
 
-We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing *wrappers* and tell nextflow about it. This is what the [src/nf_modules/cutadapt/cutadapt.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/cutadapt.config) is used for.
+We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing *wrappers* and tell nextflow about it. This is what the [src/nf_modules/cutadapt/adaptor_removal_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.config) is used for.
 
-Copy the content of this config file to an `src/RNASeq.config` file. This file is structured in process blocks. Here we are only interested in configuring `adaptor_removal` process not `trimming` process. So you can remove the `trimming` block and commit.
+Copy the content of this config file to an `src/RNASeq.config` file. This file is structured in process blocks. Here we are only interested in configuring `adaptor_removal` process not `trimming` process. So you can remove the `trimming` block and commit it.
 
 You can test your pipeline with the following command:
 
@@ -308,7 +322,7 @@ You can test your pipeline with the following command:
 
 The second step of the pipeline is to trim reads by quality.
 
-Browse for [src/nf_modules/UrQt/urqt.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/UrQt/urqt.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit.
+Browse for [src/nf_modules/urqt/trimming_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit it.
 
 This code won’t work if you try to run it: the `fastq_file` channel is already consumed by the `adaptor_removal` process. In nextflow once a channel is used by a process, it ceases to exist. Moreover, we don’t want to trim the input fastq, we want to trim the fastq that comes from the `adaptor_removal` process.
 
@@ -326,7 +340,7 @@ set pair_id, file(reads) from fastq_files_cut
 
 The two processes are now connected by the channel `fastq_files_cut`.
 
-Add the content of the [src/nf_modules/UrQt/urqt.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/UrQt/urqt.config) file to your `src/RNASeq.config` file and commit.
+Add the content of the [src/nf_modules/urqt/trimming_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config) file to your `src/RNASeq.config` file and commit it.
 
 You can test your pipeline.
 
@@ -334,7 +348,7 @@ You can test your pipeline.
 
 Kallisto need the sequences of the transcripts that need to be quantified. We are going to extract these sequences from the reference `data/tiny_dataset/fasta/tiny_v2.fasta` with the `bed` annotation `data/tiny_dataset/annot/tiny.bed`.
 
-You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/BEDtools/bedtools.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/bedtools.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/BEDtools/bedtools.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/bedtools.config).
+You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/bedtools/fasta_from_bed.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/bedtools/fasta_from_bed.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config).
 
 Commit your work and test your pipeline with the following command:
 
@@ -346,7 +360,7 @@ Commit your work and test your pipeline with the following command:
 
 Kallisto run in two steps: the indexation of the reference and the quantification on this index.
 
-You can copy to your `src/RNASeq.nf` file the relevant content of [src/nf_modules/Kallisto/kallisto.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/kallisto.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/Kallisto/kallisto.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/kallisto.config).
+You can copy to your `src/RNASeq.nf` file the content of the files [src/nf_modules/kallisto/indexing.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf) and [src/nf_modules/kallisto/mapping_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf). You can add to your file `src/RNASeq.config` file the content of the files [src/nf_modules/kallisto/indexing.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.config) and [src/nf_modules/kallisto/mapping_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config).
 
 We are going to work with paired-end so only copy the relevant processes. The `index_fasta` process needs to take as input the output of your `fasta_from_bed` process. The `fastq` input of your `mapping_fastq` process needs to take as input the output of your `index_fasta` process and the `trimming` process.
 
@@ -384,12 +398,21 @@ ln -s /Xnfs/lbmcdb/common/modules/modulefiles ~/privatemodules
 echo "module use ~/privatemodules" >> .bashrc
 ```
 
+Create and go to your `scratch` folder:
+
+```sh
+mkdir -p /scratch/<login>
+cd /scratch/<login>
+echo "module use ~/privatemodules" >> .bashrc
+```
+
 Then you need to clone your pipeline and get the data:
 
 ```sh
-git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/lmodolo/nextflow.git
+git config --global http.sslVerify false
+git clone https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
 cd nextflow/data
-git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
 cd ..
 ```
 
@@ -400,13 +423,13 @@ As we don’t want nextflow to be killed in case of disconnection, we start by l
 ```sh
 tmux
 module load nextflow/0.28.2
-nextflow src/RNASeq.nf -c src/RNASeq.config -profile sge --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed"
+nextflow src/RNASeq.nf -c src/RNASeq.config -profile psmn --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -w /scratch/<login>
 ```
 
 To use the scratch for nextflow computations add the option :
 
 ```sh
--w /scratch/login
+-w /scratch/<login>
 ```
 
 You just ran your pipeline on the PSMN!
diff --git a/src/docker_modules/BEDtools/2.25.0/docker_init.sh b/src/docker_modules/BEDtools/2.25.0/docker_init.sh
deleted file mode 100755
index c5c6f802290d6b629a949de8962709e3c5d7f258..0000000000000000000000000000000000000000
--- a/src/docker_modules/BEDtools/2.25.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'
diff --git a/src/docker_modules/Bowtie/1.2.2/docker_init.sh b/src/docker_modules/Bowtie/1.2.2/docker_init.sh
deleted file mode 100755
index 8e010a67b74c0e5519d639c3cb06a14c1fb6f987..0000000000000000000000000000000000000000
--- a/src/docker_modules/Bowtie/1.2.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Bowtie/1.2.2 -t 'bowtie:1.2.2'
diff --git a/src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh b/src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh
deleted file mode 100755
index bba04c2bded6ebb0ba035ebead94b45effc7f486..0000000000000000000000000000000000000000
--- a/src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
diff --git a/src/docker_modules/FastQC/0.11.5/docker_init.sh b/src/docker_modules/FastQC/0.11.5/docker_init.sh
deleted file mode 100755
index d8d557f5a93c4d163686285b8d5c0123006b3750..0000000000000000000000000000000000000000
--- a/src/docker_modules/FastQC/0.11.5/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'
diff --git a/src/docker_modules/HISAT2/2.0.0/docker_init.sh b/src/docker_modules/HISAT2/2.0.0/docker_init.sh
deleted file mode 100755
index f497a67af04b382913f516d2b0fa78c4a00a0d26..0000000000000000000000000000000000000000
--- a/src/docker_modules/HISAT2/2.0.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/HISAT2/2.0.0 -t 'hisat2:2.0.0'
diff --git a/src/docker_modules/HTSeq/0.8.0/docker_init.sh b/src/docker_modules/HTSeq/0.8.0/docker_init.sh
deleted file mode 100755
index 5b8415e2d4adeb65314a29d7cf7d386eba96e6cc..0000000000000000000000000000000000000000
--- a/src/docker_modules/HTSeq/0.8.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'
diff --git a/src/docker_modules/Kallisto/0.43.1/docker_init.sh b/src/docker_modules/Kallisto/0.43.1/docker_init.sh
deleted file mode 100755
index 8904daee8e494a755d44ab85f935c209ef80e5e1..0000000000000000000000000000000000000000
--- a/src/docker_modules/Kallisto/0.43.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'
diff --git a/src/docker_modules/Kallisto/0.44.0/docker_init.sh b/src/docker_modules/Kallisto/0.44.0/docker_init.sh
deleted file mode 100755
index a17b82f5761976daacd7b909998af2f600264136..0000000000000000000000000000000000000000
--- a/src/docker_modules/Kallisto/0.44.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/MACS2/2.1.0/Dockerfile b/src/docker_modules/MACS2/2.1.0/Dockerfile
deleted file mode 100644
index faf2e9088ce84eadc75612627cf74aa7fd2c7381..0000000000000000000000000000000000000000
--- a/src/docker_modules/MACS2/2.1.0/Dockerfile
+++ /dev/null
@@ -1,20 +0,0 @@
-FROM ubuntu:18.04
-MAINTAINER Laurent Modolo
-
-ENV MACS_VERSION=2.1.1.20160309
-ENV PACKAGES git=1:2.17* \
-   build-essential=12.4* \
-   python-pip=9.0.1* \
-   ca-certificates=20180409 \
-   python-setuptools=39.0.1* \
-   python-dev=2.7* \
-   python-numpy=1:1.13* \
-   python-wheel=0.30.0* \
-   zlib1g-dev=1:1.2.11*
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
-
-RUN pip install MACS2==${MACS_VERSION}
-
diff --git a/src/docker_modules/MACS2/2.1.0/docker_init.sh b/src/docker_modules/MACS2/2.1.0/docker_init.sh
deleted file mode 100755
index 8af6fd7fe7139608a894fc053f987e6ef4b3380a..0000000000000000000000000000000000000000
--- a/src/docker_modules/MACS2/2.1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/MACS2/2.1.0 -t 'macs2:2.1.0'
diff --git a/src/docker_modules/MUSIC/6613c53/Dockerfile b/src/docker_modules/MUSIC/6613c53/Dockerfile
deleted file mode 100644
index 0c6f4e4c018d75cafc0812278fb9899b354d4da2..0000000000000000000000000000000000000000
--- a/src/docker_modules/MUSIC/6613c53/Dockerfile
+++ /dev/null
@@ -1,25 +0,0 @@
-FROM samtools:1.7
-MAINTAINER Laurent Modolo
-
-ENV PACKAGES git=1:2.17* \
-   build-essential=12.4* \
-   ca-certificates=20180409 \
-   zlib1g-dev=1:1.2.11*
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
-
-RUN git clone https://github.com/gersteinlab/MUSIC.git && \
-  cd MUSIC && \
-  git checkout ${MUSIC_VERSION} && \
-  make clean && \
-  make  && \
-  cd .. && \
-  mv MUSIC/bin/MUSIC /usr/bin/ && \
-  mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
-  mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
-  rm -Rf MUSIC
-
-RUN chmod +x /usr/bin/*
-
diff --git a/src/docker_modules/MUSIC/6613c53/docker_init.sh b/src/docker_modules/MUSIC/6613c53/docker_init.sh
deleted file mode 100755
index c6163d6b58877cd3a7fd31be65fa2b9ee958c3d5..0000000000000000000000000000000000000000
--- a/src/docker_modules/MUSIC/6613c53/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/MUSIC/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/MultiQC/1.0/docker_init.sh b/src/docker_modules/MultiQC/1.0/docker_init.sh
deleted file mode 100755
index 7fb1b64ef11994fa6d555bf125242399dd7fce18..0000000000000000000000000000000000000000
--- a/src/docker_modules/MultiQC/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/MultiQC/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/RSEM/1.3.0/docker_init.sh b/src/docker_modules/RSEM/1.3.0/docker_init.sh
deleted file mode 100755
index 5d788282b75adba0b372667e3a458a90b6aa4bfe..0000000000000000000000000000000000000000
--- a/src/docker_modules/RSEM/1.3.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/RSEM/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/SAMtools/1.7/docker_init.sh b/src/docker_modules/SAMtools/1.7/docker_init.sh
deleted file mode 100755
index 31916f45aa54dac20237de987b065153cd6022d9..0000000000000000000000000000000000000000
--- a/src/docker_modules/SAMtools/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/SAMtools/1.7 -t 'samtools:1.7'
diff --git a/src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh b/src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh
deleted file mode 100755
index 501f769edecaf06b7a967d8b3aaecfb8e0ff7454..0000000000000000000000000000000000000000
--- a/src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/Salmon/0.8.2/docker_init.sh b/src/docker_modules/Salmon/0.8.2/docker_init.sh
deleted file mode 100755
index ea75cf11004089375ff2dc56b619b08cb51955b2..0000000000000000000000000000000000000000
--- a/src/docker_modules/Salmon/0.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/TopHat/2.1.1/docker_init.sh b/src/docker_modules/TopHat/2.1.1/docker_init.sh
deleted file mode 100755
index 55e782f2fa5f6e45216c50fc86bc360fb8fa61b2..0000000000000000000000000000000000000000
--- a/src/docker_modules/TopHat/2.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/TopHat/2.1.1 -t 'tophat:2.1.1'
diff --git a/src/docker_modules/Trimmomatic/0.36/docker_init.sh b/src/docker_modules/Trimmomatic/0.36/docker_init.sh
deleted file mode 100755
index dd5c050d1c12a0a60b836e395a88f5a1a1f6e061..0000000000000000000000000000000000000000
--- a/src/docker_modules/Trimmomatic/0.36/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/Trimmomatic/0.36 -t 'trimmomatic:0.36'
diff --git a/src/docker_modules/UrQt/d62c1f8/docker_init.sh b/src/docker_modules/UrQt/d62c1f8/docker_init.sh
deleted file mode 100755
index 225589e021b151416048a8cf13f47bd3daa257d4..0000000000000000000000000000000000000000
--- a/src/docker_modules/UrQt/d62c1f8/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/UrQt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/docker_modules/SAMtools/1.7/Dockerfile b/src/docker_modules/bcftools/1.7/Dockerfile
similarity index 69%
rename from src/docker_modules/SAMtools/1.7/Dockerfile
rename to src/docker_modules/bcftools/1.7/Dockerfile
index ce910af725ef312491a610db21989b2041846612..b602f187b41a8d54429b06ca45822482292ed68a 100644
--- a/src/docker_modules/SAMtools/1.7/Dockerfile
+++ b/src/docker_modules/bcftools/1.7/Dockerfile
@@ -1,8 +1,8 @@
 FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
-ENV SAMTOOLS_VERSION=1.7
-ENV PACKAGES samtools=${SAMTOOLS_VERSION}*
+ENV BCFTOOLS_VERSION=1.7
+ENV PACKAGES bcftools=${BCFTOOLS_VERSION}*
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \
diff --git a/src/docker_modules/bcftools/1.7/docker_init.sh b/src/docker_modules/bcftools/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6d19c6899eebecf2dcd8270ca2aa042a507a74ea
--- /dev/null
+++ b/src/docker_modules/bcftools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bcftools/1.7 -t 'bcftools:1.7'
diff --git a/src/docker_modules/BEDtools/2.25.0/Dockerfile b/src/docker_modules/bedtools/2.25.0/Dockerfile
similarity index 100%
rename from src/docker_modules/BEDtools/2.25.0/Dockerfile
rename to src/docker_modules/bedtools/2.25.0/Dockerfile
diff --git a/src/docker_modules/bedtools/2.25.0/docker_init.sh b/src/docker_modules/bedtools/2.25.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..63da76f2df7e2210f8e97c57b32f5c4ae010e394
--- /dev/null
+++ b/src/docker_modules/bedtools/2.25.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bedtools/2.25.0 -t 'bedtools:2.25.0'
diff --git a/src/docker_modules/bioawk/1.0/Dockerfile b/src/docker_modules/bioawk/1.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..f7ca9803e60926ed90bce0abfe4cf7af90d72672
--- /dev/null
+++ b/src/docker_modules/bioawk/1.0/Dockerfile
@@ -0,0 +1,21 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BIOAWK_VERSION=1.0
+ENV PACKAGES git=1:2.17* \
+   build-essential=12.4* \
+   ca-certificates=20180409 \
+   zlib1g-dev=1:1.2.11* \
+   byacc
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN git clone https://github.com/lh3/bioawk.git && \
+  cd bioawk && \
+  git checkout tags/v${BIOAWK_VERSION} && \
+  make && \
+  cd .. && \
+  mv bioawk/bioawk /usr/bin/ && \
+  rm -Rf bioawk
diff --git a/src/docker_modules/bioawk/1.0/docker_init.sh b/src/docker_modules/bioawk/1.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..23c163352f6d380d6dcb0accb6de24d8281af8b6
--- /dev/null
+++ b/src/docker_modules/bioawk/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bioawk/1.0 -t 'bioawk:1.0'
diff --git a/src/docker_modules/Bowtie/1.2.2/Dockerfile b/src/docker_modules/bowtie/1.2.2/Dockerfile
similarity index 100%
rename from src/docker_modules/Bowtie/1.2.2/Dockerfile
rename to src/docker_modules/bowtie/1.2.2/Dockerfile
diff --git a/src/docker_modules/bowtie/1.2.2/docker_init.sh b/src/docker_modules/bowtie/1.2.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c8106dbf08e45df38e05b3dda6fb0e20dcec238b
--- /dev/null
+++ b/src/docker_modules/bowtie/1.2.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie/1.2.2 -t 'bowtie:1.2.2'
diff --git a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile b/src/docker_modules/bowtie2/2.3.4.1/Dockerfile
similarity index 100%
rename from src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
rename to src/docker_modules/bowtie2/2.3.4.1/Dockerfile
diff --git a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..77141d11131d21f7705aba955c271a2171a077d7
--- /dev/null
+++ b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/Dockerfile b/src/docker_modules/bwa/0.7.17/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..7a538498bc4a1489f31fe2692224c02203042c44
--- /dev/null
+++ b/src/docker_modules/bwa/0.7.17/Dockerfile
@@ -0,0 +1,30 @@
+FROM sambamba:0.6.7
+MAINTAINER Laurent Modolo
+
+ENV BWA_VERSION=0.7.17
+ENV SAMBLASTER_VERSION=0.1.24
+
+ENV PACKAGES curl=7.58.0* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
+tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
+cd bwa-${BWA_VERSION}/ && \
+make && \
+cp bwa /usr/bin && \
+cd .. && \
+rm -R bwa-${BWA_VERSION}/
+
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
diff --git a/src/docker_modules/bwa/0.7.17/docker_init.sh b/src/docker_modules/bwa/0.7.17/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d20312207e76e0dfd076e4130209dff1bbdd677e
--- /dev/null
+++ b/src/docker_modules/bwa/0.7.17/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bwa/0.7.17 -t 'bwa:0.7.17'
diff --git a/src/docker_modules/cutadapt/1.14/Dockerfile b/src/docker_modules/cutadapt/1.14/Dockerfile
index b8c5f54f41d5d349453fdb7062e9a1d3f0639c10..35d23b7b235d3ad1e611af9287c92d9147f8e440 100644
--- a/src/docker_modules/cutadapt/1.14/Dockerfile
+++ b/src/docker_modules/cutadapt/1.14/Dockerfile
@@ -1,15 +1,14 @@
-FROM ubuntu:18.04
+FROM alpine:3.8
 MAINTAINER Laurent Modolo
 
 ENV CUTADAPT_VERSION=1.14
-ENV PACKAGES build-essential=12.4* \
-             python3-pip=9.0.1* \
-             python3-setuptools=39.0.1* \
-             python3-dev=3.6.5* \
-             python3-wheel=0.30.0*
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
+RUN apk update && \
+    apk add ${PACKAGES}
 
 RUN pip3 install cutadapt==${CUTADAPT_VERSION}
diff --git a/src/docker_modules/cutadapt/1.15/Dockerfile b/src/docker_modules/cutadapt/1.15/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..96bbd20ded423656458885b2522348711a838e97
--- /dev/null
+++ b/src/docker_modules/cutadapt/1.15/Dockerfile
@@ -0,0 +1,14 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=1.15
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}
diff --git a/src/docker_modules/cutadapt/1.15/docker_init.sh b/src/docker_modules/cutadapt/1.15/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..b3cf541353b3f5e2035e8a9b71123572c382cc88
--- /dev/null
+++ b/src/docker_modules/cutadapt/1.15/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.15 -t 'cutadapt:1.15'
diff --git a/src/docker_modules/deepTools/3.0.2/Dockerfile b/src/docker_modules/deepTools/3.0.2/Dockerfile
deleted file mode 100644
index c358701fcdba8080469c77b9a5a4bc581d8e0ae4..0000000000000000000000000000000000000000
--- a/src/docker_modules/deepTools/3.0.2/Dockerfile
+++ /dev/null
@@ -1,17 +0,0 @@
-FROM ubuntu:18.04
-MAINTAINER Laurent Modolo
-
-ENV DEEPTOOLS_VERSION=3.0.2
-ENV PACKAGES build-essential=12.4* \
-             python3-pip=9.0.1* \
-             python3-setuptools=39.0.1* \
-             python3-dev=3.6.5* \
-             python3-wheel=0.30.0* \
-             zlib1g-dev=1:1.2.11* \
-             libcurl4-gnutls-dev=7.58.0*
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
-
-RUN pip3 install deeptools==${DEEPTOOLS_VERSION}
diff --git a/src/docker_modules/deepTools/3.0.2/docker_init.sh b/src/docker_modules/deepTools/3.0.2/docker_init.sh
deleted file mode 100755
index ed0f069b1a759e5e13566add9212c853ca27df49..0000000000000000000000000000000000000000
--- a/src/docker_modules/deepTools/3.0.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/deepTools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.0.2/Dockerfile b/src/docker_modules/deeptools/3.0.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..adc170057075eb7c76dfc67b41039b5875a5d963
--- /dev/null
+++ b/src/docker_modules/deeptools/3.0.2/Dockerfile
@@ -0,0 +1,17 @@
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV DEEPTOOLS_VERSION=3.0.2
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             libcurl4-gnutls-dev
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install deeptools==${DEEPTOOLS_VERSION}
diff --git a/src/docker_modules/deeptools/3.0.2/docker_init.sh b/src/docker_modules/deeptools/3.0.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a2f152d2de03155d2055db8f8bdeb0c8585e135c
--- /dev/null
+++ b/src/docker_modules/deeptools/3.0.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/Dockerfile b/src/docker_modules/deeptools/3.1.1/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..2e84a709cd0078765070d284e5119e236b251283
--- /dev/null
+++ b/src/docker_modules/deeptools/3.1.1/Dockerfile
@@ -0,0 +1,19 @@
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV DEEPTOOLS_VERSION=3.1.1
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             libcurl4-gnutls-dev \
+             procps
+
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install deeptools==${DEEPTOOLS_VERSION}
diff --git a/src/docker_modules/deeptools/3.1.1/docker_init.sh b/src/docker_modules/deeptools/3.1.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3c6782f0dd688006bafd2d59d3a2ff52a3f03a32
--- /dev/null
+++ b/src/docker_modules/deeptools/3.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.1.1 -t 'deeptools:3.1.1'
diff --git a/src/docker_modules/fastp/0.19.7/Dockerfile b/src/docker_modules/fastp/0.19.7/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..234995a7b43807c45e673f6fc64677123cdfd67f
--- /dev/null
+++ b/src/docker_modules/fastp/0.19.7/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
+MAINTAINER Laurent Modolo
diff --git a/src/docker_modules/fastp/0.19.7/docker_init.sh b/src/docker_modules/fastp/0.19.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0480706aced0568e65e54270aacdfe0c89347b34
--- /dev/null
+++ b/src/docker_modules/fastp/0.19.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastp/0.19.7 -t 'fastp:0.19.7'
diff --git a/src/docker_modules/FastQC/0.11.5/Dockerfile b/src/docker_modules/fastqc/0.11.5/Dockerfile
similarity index 100%
rename from src/docker_modules/FastQC/0.11.5/Dockerfile
rename to src/docker_modules/fastqc/0.11.5/Dockerfile
diff --git a/src/docker_modules/fastqc/0.11.5/docker_init.sh b/src/docker_modules/fastqc/0.11.5/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0c02fb709b3e9993124e08d88aec5700a0e32afb
--- /dev/null
+++ b/src/docker_modules/fastqc/0.11.5/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastqc/0.11.5 -t 'fastqc:0.11.5'
diff --git a/src/docker_modules/gatk/4.0.8.1/Dockerfile b/src/docker_modules/gatk/4.0.8.1/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..aceded338897254a31dca826413b63cffd933532
--- /dev/null
+++ b/src/docker_modules/gatk/4.0.8.1/Dockerfile
@@ -0,0 +1,6 @@
+FROM broadinstitute/gatk:4.0.8.1
+MAINTAINER Laurent Modolo
+
+ENV GATK_VERSION=4.0.8.1
+
+RUN cp gatk /usr/bin/
diff --git a/src/docker_modules/gatk/4.0.8.1/docker_init.sh b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..31315f92ab7c76d59dc81f9eaf3c2ebb827ca38a
--- /dev/null
+++ b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/gatk/4.0.8.1 -t 'gatk:4.0.8.1'
diff --git a/src/docker_modules/HISAT2/2.0.0/Dockerfile b/src/docker_modules/hisat2/2.0.0/Dockerfile
similarity index 100%
rename from src/docker_modules/HISAT2/2.0.0/Dockerfile
rename to src/docker_modules/hisat2/2.0.0/Dockerfile
diff --git a/src/docker_modules/hisat2/2.0.0/docker_init.sh b/src/docker_modules/hisat2/2.0.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..428e28c464f38210862cf09e8f370d5bfbcb8357
--- /dev/null
+++ b/src/docker_modules/hisat2/2.0.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.0.0 -t 'hisat2:2.0.0'
diff --git a/src/docker_modules/HTSeq/0.8.0/Dockerfile b/src/docker_modules/htseq/0.8.0/Dockerfile
similarity index 60%
rename from src/docker_modules/HTSeq/0.8.0/Dockerfile
rename to src/docker_modules/htseq/0.8.0/Dockerfile
index a786b8026f66e9538c543f79624325ccb75952c6..492d91a697b945a3acd3aa3bd0ebb09590fb3de5 100644
--- a/src/docker_modules/HTSeq/0.8.0/Dockerfile
+++ b/src/docker_modules/htseq/0.8.0/Dockerfile
@@ -3,11 +3,11 @@ FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
 ENV HTSEQ_VERSION=0.8.0
-ENV PACKAGES build-essential=12.4* \
-             python3-pip=9.0.1* \
-             python3-setuptools=39.0.1* \
-             python3-dev=3.6.5* \
-             python3-wheel=0.30.0*
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \
diff --git a/src/docker_modules/htseq/0.8.0/docker_init.sh b/src/docker_modules/htseq/0.8.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..be46648e419daabc1e382da0885fafddd129f73c
--- /dev/null
+++ b/src/docker_modules/htseq/0.8.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.8.0 -t 'htseq:0.8.0'
diff --git a/src/docker_modules/Kallisto/0.43.1/Dockerfile b/src/docker_modules/kallisto/0.43.1/Dockerfile
similarity index 100%
rename from src/docker_modules/Kallisto/0.43.1/Dockerfile
rename to src/docker_modules/kallisto/0.43.1/Dockerfile
diff --git a/src/docker_modules/kallisto/0.43.1/docker_init.sh b/src/docker_modules/kallisto/0.43.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..08241603199a137dd3b6bcf52d53b239c237145a
--- /dev/null
+++ b/src/docker_modules/kallisto/0.43.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.43.1 -t 'kallisto:0.43.1'
diff --git a/src/docker_modules/Kallisto/0.44.0/Dockerfile b/src/docker_modules/kallisto/0.44.0/Dockerfile
similarity index 100%
rename from src/docker_modules/Kallisto/0.44.0/Dockerfile
rename to src/docker_modules/kallisto/0.44.0/Dockerfile
diff --git a/src/docker_modules/kallisto/0.44.0/docker_init.sh b/src/docker_modules/kallisto/0.44.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9e9e8c91350215ab62b815d3277fb75bcda9a6b5
--- /dev/null
+++ b/src/docker_modules/kallisto/0.44.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.2/Dockerfile b/src/docker_modules/macs2/2.1.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..71979a50044cd8ce9c52f1d413db269088d352dd
--- /dev/null
+++ b/src/docker_modules/macs2/2.1.2/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1
+MAINTAINER Laurent Modolo
diff --git a/src/docker_modules/macs2/2.1.2/docker_init.sh b/src/docker_modules/macs2/2.1.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2cd63afd9e01edb8c4c6fa1e9021db82b3196503
--- /dev/null
+++ b/src/docker_modules/macs2/2.1.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/macs2/2.1.2 -t 'macs2:2.1.2'
diff --git a/src/docker_modules/MultiQC/1.0/Dockerfile b/src/docker_modules/multiqc/1.0/Dockerfile
similarity index 56%
rename from src/docker_modules/MultiQC/1.0/Dockerfile
rename to src/docker_modules/multiqc/1.0/Dockerfile
index d351f1c6a979de6616edce3fd276be262bad8b43..7acf600c99d9f3500bf015d4b79e3675ac5d7789 100644
--- a/src/docker_modules/MultiQC/1.0/Dockerfile
+++ b/src/docker_modules/multiqc/1.0/Dockerfile
@@ -1,12 +1,13 @@
-FROM ubuntu:18.04
+FROM debian:stretch
 MAINTAINER Laurent Modolo
 
 ENV MULTIQC_VERSION=1.0
-ENV PACKAGES build-essential=12.4* \
-             python3-pip=9.0.1* \
-             python3-setuptools=39.0.1* \
-             python3-dev=3.6.5* \
-             python3-wheel=0.30.0* \
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
              locales
 
 RUN apt-get update && \
@@ -16,6 +17,9 @@ RUN apt-get update && \
 RUN locale-gen en_US.UTF-8
 ENV LC_ALL=en_US.utf-8
 ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
 
 RUN pip3 install multiqc==${MULTIQC_VERSION}
 
diff --git a/src/docker_modules/multiqc/1.0/docker_init.sh b/src/docker_modules/multiqc/1.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4c6de82afe5a0ce476399875ed701966da319f27
--- /dev/null
+++ b/src/docker_modules/multiqc/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/multiqc/1.7/Dockerfile b/src/docker_modules/multiqc/1.7/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..ea71b1ad8227b9456863b7b00fc5d818db090288
--- /dev/null
+++ b/src/docker_modules/multiqc/1.7/Dockerfile
@@ -0,0 +1,25 @@
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.7
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+
diff --git a/src/docker_modules/multiqc/1.7/docker_init.sh b/src/docker_modules/multiqc/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..67ff4536e50e7e87f049359916d5136db56663a2
--- /dev/null
+++ b/src/docker_modules/multiqc/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.7 -t 'multiqc:1.7'
diff --git a/src/docker_modules/music/6613c53/Dockerfile b/src/docker_modules/music/6613c53/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..aa47eb572ca48736457bb0f60b0857bbe6c5d9df
--- /dev/null
+++ b/src/docker_modules/music/6613c53/Dockerfile
@@ -0,0 +1,38 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV MUSIC_VERSION=6613c53
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES g++ \
+bash \
+pcre-dev \
+openssl-dev \
+build-base \
+bzip2-dev \
+xz-dev \
+git \
+curl
+
+RUN apk update && \
+    apk add ${PACKAGES}
+RUN curl -L -o samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+    http://jaist.dl.sourceforge.net/project/samtools/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && tar jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2  \
+ && cd samtools-${SAMTOOLS_VERSION}/ \
+ && ./configure --without-curses \
+ && make \
+ && make install
+
+RUN git clone https://github.com/gersteinlab/MUSIC.git && \
+  cd MUSIC && \
+  git checkout ${MUSIC_VERSION} && \
+  make clean && \
+  make  && \
+  cd .. && \
+  mv MUSIC/bin/MUSIC /usr/bin/ && \
+  mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
+  mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
+  rm -Rf MUSIC
+
+RUN chmod +x /usr/bin/*
+
diff --git a/src/docker_modules/music/6613c53/docker_init.sh b/src/docker_modules/music/6613c53/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5daa39f1013e09253b8c52e1e481c4462e45cf26
--- /dev/null
+++ b/src/docker_modules/music/6613c53/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/music/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/RSEM/1.3.0/Dockerfile b/src/docker_modules/rsem/1.3.0/Dockerfile
similarity index 100%
rename from src/docker_modules/RSEM/1.3.0/Dockerfile
rename to src/docker_modules/rsem/1.3.0/Dockerfile
diff --git a/src/docker_modules/rsem/1.3.0/docker_init.sh b/src/docker_modules/rsem/1.3.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..02d4bf9cc127f2a4ccc8592efd7c2aa79b28461b
--- /dev/null
+++ b/src/docker_modules/rsem/1.3.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/rsem/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/Salmon/0.8.2/Dockerfile b/src/docker_modules/salmon/0.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/Salmon/0.8.2/Dockerfile
rename to src/docker_modules/salmon/0.8.2/Dockerfile
diff --git a/src/docker_modules/salmon/0.8.2/docker_init.sh b/src/docker_modules/salmon/0.8.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5abdc6b06e792e0eb5c89248e8a240844bdd8a1a
--- /dev/null
+++ b/src/docker_modules/salmon/0.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/sambamba/0.6.7/Dockerfile b/src/docker_modules/sambamba/0.6.7/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..5858a176917fc301e165ba18a6d69c34a1bf786a
--- /dev/null
+++ b/src/docker_modules/sambamba/0.6.7/Dockerfile
@@ -0,0 +1,17 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV SAMBAMBA_VERSION=0.6.7
+ENV PACKAGES curl=7.58.0* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
diff --git a/src/docker_modules/sambamba/0.6.7/docker_init.sh b/src/docker_modules/sambamba/0.6.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2db68c5b8aec2734b47d91930c2285cb8cfe799f
--- /dev/null
+++ b/src/docker_modules/sambamba/0.6.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.7 -t 'sambamba:0.6.7'
diff --git a/src/docker_modules/samblaster/0.1.24/Dockerfile b/src/docker_modules/samblaster/0.1.24/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..dcba024b879e8ef7720e35873d9e8101116891c6
--- /dev/null
+++ b/src/docker_modules/samblaster/0.1.24/Dockerfile
@@ -0,0 +1,22 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV SAMBLASTER_VERSION=0.1.24
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES curl=7.58.0* \
+    samtools=${SAMTOOLS_VERSION}* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
diff --git a/src/docker_modules/samblaster/0.1.24/docker_init.sh b/src/docker_modules/samblaster/0.1.24/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..24927903f57b4433e501d3ec94bf83670b51c057
--- /dev/null
+++ b/src/docker_modules/samblaster/0.1.24/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samblaster/0.1.24 -t 'samblaster:0.1.24'
diff --git a/src/docker_modules/samtools/1.7/Dockerfile b/src/docker_modules/samtools/1.7/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..212101a98a9e01783e95d2db93c43d359d5f4d3a
--- /dev/null
+++ b/src/docker_modules/samtools/1.7/Dockerfile
@@ -0,0 +1,26 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES git \
+             make \
+             gcc \
+             musl-dev \
+             zlib-dev \
+             ncurses-dev \
+             bzip2-dev \
+             xz-dev \
+             bash
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION}  && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
diff --git a/src/docker_modules/samtools/1.7/docker_init.sh b/src/docker_modules/samtools/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..03dc62e9a1d56d102a2ed5e4d251509dde689edb
--- /dev/null
+++ b/src/docker_modules/samtools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samtools/1.7 -t 'samtools:1.7'
diff --git a/src/docker_modules/SRAtoolkit/2.8.2/Dockerfile b/src/docker_modules/sratoolkit/2.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/SRAtoolkit/2.8.2/Dockerfile
rename to src/docker_modules/sratoolkit/2.8.2/Dockerfile
diff --git a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..234100e8297fe288a64956074223a2185ff24bf9
--- /dev/null
+++ b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sratoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/subread/1.6.4/Dockerfile b/src/docker_modules/subread/1.6.4/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..97d5870ad4d7a59ec0e8f38300d8e86651cc2e8b
--- /dev/null
+++ b/src/docker_modules/subread/1.6.4/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/subread:1.6.4--h84994c4_1
+MAINTAINER Laurent Modolo
diff --git a/src/docker_modules/subread/1.6.4/docker_init.sh b/src/docker_modules/subread/1.6.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9c2c68569910fde8b5710fc5a5cf47c3d4bf76d9
--- /dev/null
+++ b/src/docker_modules/subread/1.6.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/subread/1.6.4 -t 'subread:1.6.4'
diff --git a/src/docker_modules/TopHat/2.1.1/Dockerfile b/src/docker_modules/tophat/2.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/TopHat/2.1.1/Dockerfile
rename to src/docker_modules/tophat/2.1.1/Dockerfile
diff --git a/src/docker_modules/tophat/2.1.1/docker_init.sh b/src/docker_modules/tophat/2.1.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4dd0937a271053c5c3b56dfb0616107c8e0188b2
--- /dev/null
+++ b/src/docker_modules/tophat/2.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/tophat/2.1.1 -t 'tophat:2.1.1'
diff --git a/src/docker_modules/Trimmomatic/0.36/Dockerfile b/src/docker_modules/trimmomatic/0.36/Dockerfile
similarity index 100%
rename from src/docker_modules/Trimmomatic/0.36/Dockerfile
rename to src/docker_modules/trimmomatic/0.36/Dockerfile
diff --git a/src/docker_modules/trimmomatic/0.36/docker_init.sh b/src/docker_modules/trimmomatic/0.36/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..63bcdabfbaa8984022afc93ef92fbf014f9ad28c
--- /dev/null
+++ b/src/docker_modules/trimmomatic/0.36/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/trimmomatic/0.36 -t 'trimmomatic:0.36'
diff --git a/src/docker_modules/ucsc/375/Dockerfile b/src/docker_modules/ucsc/375/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..8daf43a697d5fa50e1b218e66fa83462b651baf8
--- /dev/null
+++ b/src/docker_modules/ucsc/375/Dockerfile
@@ -0,0 +1,25 @@
+FROM debian:jessie
+MAINTAINER Laurent Modolo
+
+ENV PACKAGES apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             rsync
+
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES}
+
+ENV UCSC_VERSION=375
+
+RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps
diff --git a/src/docker_modules/ucsc/375/docker_init.sh b/src/docker_modules/ucsc/375/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ef314b4236476de4bc8c3735e9be51a1f3efc7c1
--- /dev/null
+++ b/src/docker_modules/ucsc/375/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/ucsc/375/ -t 'ucsc:375'
diff --git a/src/docker_modules/umitools/0.3.4/Dockerfile b/src/docker_modules/umitools/0.3.4/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..c5e417b285aa0ed0bc6e5bdd5d446d5291a77ad0
--- /dev/null
+++ b/src/docker_modules/umitools/0.3.4/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/umitools:0.3.4--py37_1
+MAINTAINER Laurent Modolo
diff --git a/src/docker_modules/umitools/0.3.4/docker_init.sh b/src/docker_modules/umitools/0.3.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4a5b59aeb0b4eac68b6e2d7930e18f20f9fb46d7
--- /dev/null
+++ b/src/docker_modules/umitools/0.3.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/umitools/0.3.4 -t 'umitools:0.3.4'
diff --git a/src/docker_modules/UrQt/d62c1f8/Dockerfile b/src/docker_modules/urqt/d62c1f8/Dockerfile
similarity index 94%
rename from src/docker_modules/UrQt/d62c1f8/Dockerfile
rename to src/docker_modules/urqt/d62c1f8/Dockerfile
index 9dc908fba18e9da9f65049ae30e17d76087984e5..0a08520a7c219e42ea04bf86f34aa0b40d049667 100644
--- a/src/docker_modules/UrQt/d62c1f8/Dockerfile
+++ b/src/docker_modules/urqt/d62c1f8/Dockerfile
@@ -1,6 +1,7 @@
 FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
+ENV URQT_VERSION=d62c1f8
 ENV PACKAGES git=1:2.17* \
    build-essential=12.4* \
    ca-certificates=20180409 \
diff --git a/src/docker_modules/urqt/d62c1f8/docker_init.sh b/src/docker_modules/urqt/d62c1f8/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4c6c52692154697df95cdbbae2dfb5f184eae35b
--- /dev/null
+++ b/src/docker_modules/urqt/d62c1f8/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/urqt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
deleted file mode 100644
index 7230defdf79531542217cfc97cf85dee1888fe91..0000000000000000000000000000000000000000
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fasta_from_bed {
-        container = "bedtools:2.25.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $fasta_from_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/BEDtools/tests.sh b/src/nf_modules/BEDtools/tests.sh
deleted file mode 100755
index 632ba5bff13f65685e3ff521f4a1496b337b55d9..0000000000000000000000000000000000000000
--- a/src/nf_modules/BEDtools/tests.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
-  -c src/nf_modules/BEDtools/fasta_from_bed.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
deleted file mode 100644
index d5851003aa4c3c95b34eb78de95e20ff17aee390..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie/indexing.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie:1.2.2"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie/1.2.2"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
deleted file mode 100644
index 86cc4bb7f3c6c553811f18ed64f03c003e4780ab..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie:1.2.2"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
deleted file mode 100644
index 86cc4bb7f3c6c553811f18ed64f03c003e4780ab..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie:1.2.2"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie/tests.sh b/src/nf_modules/Bowtie/tests.sh
deleted file mode 100755
index 803f62814bc7d12e6b595b6a17ae9e96f684b6e2..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie/tests.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-./nextflow src/nf_modules/Bowtie/indexing.nf \
-  -c src/nf_modules/Bowtie/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie/mapping_single.nf \
-  -c src/nf_modules/Bowtie/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
-  -c src/nf_modules/Bowtie/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
deleted file mode 100644
index 60f60547c31e5c6fea842e3c798940a2ba6b98c5..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie2/indexing.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
deleted file mode 100644
index a8cd2991e8775c96045263645cf98079002275b1..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
deleted file mode 100644
index a8cd2991e8775c96045263645cf98079002275b1..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Bowtie2/tests.sh b/src/nf_modules/Bowtie2/tests.sh
deleted file mode 100755
index ab1483824cd1f9755d09495cd050c45cc4a82d30..0000000000000000000000000000000000000000
--- a/src/nf_modules/Bowtie2/tests.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-./nextflow src/nf_modules/Bowtie2/indexing.nf \
-  -c src/nf_modules/Bowtie2/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
-  -c src/nf_modules/Bowtie2/mapping_single.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
-  -c src/nf_modules/Bowtie2/mapping_paired.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
deleted file mode 100644
index a6589845aa98db0b4f6eaa663246db2604eb210b..0000000000000000000000000000000000000000
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ /dev/null
@@ -1,25 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
deleted file mode 100644
index a6589845aa98db0b4f6eaa663246db2604eb210b..0000000000000000000000000000000000000000
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ /dev/null
@@ -1,25 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/FastQC/tests.sh b/src/nf_modules/FastQC/tests.sh
deleted file mode 100755
index de58b1028e221f05b7d084a7df6df5e8a077c4ec..0000000000000000000000000000000000000000
--- a/src/nf_modules/FastQC/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-./nextflow src/nf_modules/FastQC/fastqc_paired.nf \
-  -c src/nf_modules/FastQC/fastqc_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-./nextflow src/nf_modules/FastQC/fastqc_single.nf \
-  -c src/nf_modules/FastQC/fastqc_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
deleted file mode 100644
index 00f2fafb921828b21fe18d57240b9a943dcd2fb9..0000000000000000000000000000000000000000
--- a/src/nf_modules/HTSeq/htseq.config
+++ /dev/null
@@ -1,24 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam {
-        container = "samtools:1.7"
-      }
-      $counting {
-        container = "htseq:0.8.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $sort_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-      $trimming {
-        beforeScript = "module purge; module load HTSeq/0.8.0"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/HTSeq/tests.sh b/src/nf_modules/HTSeq/tests.sh
deleted file mode 100755
index 4a2b5ceb62651dc0178fd026f29cd4310ecab29b..0000000000000000000000000000000000000000
--- a/src/nf_modules/HTSeq/tests.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-./nextflow src/nf_modules/HTSeq/htseq.nf \
-  -c src/nf_modules/HTSeq/htseq.config \
-  -profile docker \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config
deleted file mode 100644
index 94c14cd210981318ff555888b96f3c43796a9c66..0000000000000000000000000000000000000000
--- a/src/nf_modules/Kallisto/indexing.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Kallisto/mapping_paired.config b/src/nf_modules/Kallisto/mapping_paired.config
deleted file mode 100644
index de674527ae0735b3797dc69fe7ae90b6557e1fa1..0000000000000000000000000000000000000000
--- a/src/nf_modules/Kallisto/mapping_paired.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config
deleted file mode 100644
index de674527ae0735b3797dc69fe7ae90b6557e1fa1..0000000000000000000000000000000000000000
--- a/src/nf_modules/Kallisto/mapping_single.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/Kallisto/tests.sh b/src/nf_modules/Kallisto/tests.sh
deleted file mode 100755
index 0f69fcc40a2cc72aba93094560b2a239d2d42a76..0000000000000000000000000000000000000000
--- a/src/nf_modules/Kallisto/tests.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-./nextflow src/nf_modules/Kallisto/indexing.nf \
-  -c src/nf_modules/Kallisto/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Kallisto/mapping_single.nf \
-  -c src/nf_modules/Kallisto/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Kallisto/mapping_paired.nf \
-  -c src/nf_modules/Kallisto/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
deleted file mode 100644
index 4685752be3d8e66da4e76aeffc82ce58d50389b3..0000000000000000000000000000000000000000
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ /dev/null
@@ -1,30 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $compute_mappability {
-        container = "music:6613c53"
-      }
-      $music_preprocessing {
-        container = "music:6613c53"
-      }
-      $music_computation {
-        container = "music:6613c53"
-      }
-    }
-  }
-  sge {
-    process{
-      $compute_mappability {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_preprocessing {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_computation {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/MUSIC/tests.sh b/src/nf_modules/MUSIC/tests.sh
deleted file mode 100755
index 7c6ad078ad2c27cbb378f8cdd6c505be9527fdef..0000000000000000000000000000000000000000
--- a/src/nf_modules/MUSIC/tests.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
-./nextflow src/nf_modules/MUSIC/peak_calling_single.nf \
-  -c src/nf_modules/MUSIC/peak_calling_single.config \
-  -profile docker \
-  --fasta "results/training/fasta/*.fasta" \
-  --bam "results/training/bams/s*.bam" \
-  --index "results/training/mapping/index/*" \
-  --read_size 50 --frag_size 300
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
deleted file mode 100644
index c1bda95e70a612c7caf4825930e740faedd1c62d..0000000000000000000000000000000000000000
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ /dev/null
@@ -1,38 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-      $multiqc {
-        container = "multiqc:1.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-      $multiqc {
-        beforeScript = "module purge; module load FastQC/1.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
deleted file mode 100644
index c1bda95e70a612c7caf4825930e740faedd1c62d..0000000000000000000000000000000000000000
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ /dev/null
@@ -1,38 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-      $multiqc {
-        container = "multiqc:1.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-      $multiqc {
-        beforeScript = "module purge; module load FastQC/1.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/MultiQC/tests.sh b/src/nf_modules/MultiQC/tests.sh
deleted file mode 100755
index 0e38a8e9e9710ec9e0d43a15432c8c8e96c0dfe0..0000000000000000000000000000000000000000
--- a/src/nf_modules/MultiQC/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-./nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
-  -c src/nf_modules/MultiQC/multiqc_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-./nextflow src/nf_modules/MultiQC/multiqc_single.nf \
-  -c src/nf_modules/MultiQC/multiqc_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
deleted file mode 100644
index ddf93b6ec57c876681fc508a737b3287e20fdd61..0000000000000000000000000000000000000000
--- a/src/nf_modules/RSEM/indexing.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
deleted file mode 100644
index 344ab1e30497454826a5e45537f0e8182fb8dc63..0000000000000000000000000000000000000000
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
deleted file mode 100644
index 344ab1e30497454826a5e45537f0e8182fb8dc63..0000000000000000000000000000000000000000
--- a/src/nf_modules/RSEM/quantification_single.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/RSEM/tests.sh b/src/nf_modules/RSEM/tests.sh
deleted file mode 100755
index 7d56b790607b7cc1128262f6439cb2b4d3d012ef..0000000000000000000000000000000000000000
--- a/src/nf_modules/RSEM/tests.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-./nextflow src/nf_modules/RSEM/indexing.nf \
-  -c src/nf_modules/RSEM/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gff"
-
-./nextflow src/nf_modules/RSEM/quantification_single.nf \
-  -c src/nf_modules/RSEM/quantification_single.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/RSEM/quantification_paired.nf \
-  -c src/nf_modules/RSEM/quantification_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
deleted file mode 100644
index 066684006e4a04daef5caf26e45ba74878bb4ebf..0000000000000000000000000000000000000000
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $filter_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $filter_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
deleted file mode 100644
index 3b23601d9566ee96f034d14a798c6c8e08a6870f..0000000000000000000000000000000000000000
--- a/src/nf_modules/SAMtools/index_bams.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
deleted file mode 100644
index d1a8c503ace81d53fa5ff9cd382a435ac710e0cf..0000000000000000000000000000000000000000
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $sort_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
deleted file mode 100644
index 28b548efd5177e7457bd642b0c78198f2b48acd9..0000000000000000000000000000000000000000
--- a/src/nf_modules/SAMtools/split_bams.config
+++ /dev/null
@@ -1,18 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $split_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $split_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/SAMtools/tests.sh b/src/nf_modules/SAMtools/tests.sh
deleted file mode 100755
index 9b7ac5e47388ea99ecf137ddd6add0b2ad313149..0000000000000000000000000000000000000000
--- a/src/nf_modules/SAMtools/tests.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-./nextflow src/nf_modules/SAMtools/sort_bams.nf \
-  -c src/nf_modules/SAMtools/sort_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-./nextflow src/nf_modules/SAMtools/index_bams.nf \
-  -c src/nf_modules/SAMtools/index_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-
-./nextflow src/nf_modules/SAMtools/split_bams.nf \
-  -c src/nf_modules/SAMtools/split_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-./nextflow src/nf_modules/SAMtools/filter_bams.nf \
-  -c src/nf_modules/SAMtools/filter_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  --bed "data/tiny_dataset/OLD/2genes.bed"
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
deleted file mode 100644
index 128a4fef272aeb70993f5b614e0c34f901fc0c60..0000000000000000000000000000000000000000
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ /dev/null
@@ -1,25 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastq_dump {
-        container = "sratoolkit:2.8.2"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastq_dump {
-        beforeScript = "module purge; module load SRAtoolkit/2.8.2"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/SRAtoolkit/tests.sh b/src/nf_modules/SRAtoolkit/tests.sh
deleted file mode 100755
index d8575eb43181382f580699f5afd73f0ed69b9a2c..0000000000000000000000000000000000000000
--- a/src/nf_modules/SRAtoolkit/tests.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-./nextflow src/nf_modules/SRAtoolkit/fastqdump.nf \
-  -c src/nf_modules/SRAtoolkit/fastqdump.config \
-  -profile docker \
-  --list_srr "src/nf_modules/SRAtoolkit/list-srr.txt"
diff --git a/src/nf_modules/UrQt/tests.sh b/src/nf_modules/UrQt/tests.sh
deleted file mode 100755
index 96f5845311afe29a8d5043bf7556b3d4331b045b..0000000000000000000000000000000000000000
--- a/src/nf_modules/UrQt/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-./nextflow src/nf_modules/UrQt/trimming_paired.nf \
-  -c src/nf_modules/UrQt/trimming_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-./nextflow src/nf_modules/UrQt/trimming_single.nf \
-  -c src/nf_modules/UrQt/trimming_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
deleted file mode 100644
index 46a86729f1367966225fcb37c5ef7f11070c7255..0000000000000000000000000000000000000000
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
deleted file mode 100644
index 46a86729f1367966225fcb37c5ef7f11070c7255..0000000000000000000000000000000000000000
--- a/src/nf_modules/UrQt/trimming_single.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
deleted file mode 100644
index 46a86729f1367966225fcb37c5ef7f11070c7255..0000000000000000000000000000000000000000
--- a/src/nf_modules/UrQt/urqt.config
+++ /dev/null
@@ -1,26 +0,0 @@
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
new file mode 100644
index 0000000000000000000000000000000000000000..1875f439afb83ec770c22556d488024135cfda53
--- /dev/null
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fasta_from_bed {
+        container = "bedtools:2.25.0"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fasta_from_bed {
+        container = "file://bin/bedtools:2.25.0.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fasta_from_bed {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bedtools/2.25.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.nf b/src/nf_modules/bedtools/fasta_from_bed.nf
similarity index 99%
rename from src/nf_modules/BEDtools/fasta_from_bed.nf
rename to src/nf_modules/bedtools/fasta_from_bed.nf
index 297fd9ef429ce83c601e96f9842e940da22266b5..5e7504dcd35f29e44964e629ef8fba894c633224 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.nf
+++ b/src/nf_modules/bedtools/fasta_from_bed.nf
@@ -23,7 +23,6 @@ Channel
 
 process fasta_from_bed {
   tag "${bed.baseName}"
-  cpus 4
   publishDir "results/fasta/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bedtools/tests.sh b/src/nf_modules/bedtools/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..61b3cc9c44bad7f171e87f180f2a2a156009d48f
--- /dev/null
+++ b/src/nf_modules/bedtools/tests.sh
@@ -0,0 +1,15 @@
+./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
+  -c src/nf_modules/bedtools/fasta_from_bed.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
+  -c src/nf_modules/bedtools/fasta_from_bed.config \
+  -profile singularity \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
+fi
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..715847fb1031980d9bb7a4ef6ebd14a366cce717
--- /dev/null
+++ b/src/nf_modules/bowtie/indexing.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        cpus = 4
+        container = "bowtie:1.2.2"
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        cpus = 4
+        container = "file://bin/bowtie:1.2.2.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie/1.2.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        memory = "20GB"
+        cpus = 16
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie/indexing.nf b/src/nf_modules/bowtie/indexing.nf
similarity index 98%
rename from src/nf_modules/Bowtie/indexing.nf
rename to src/nf_modules/bowtie/indexing.nf
index 537d684b4bb39412eccfe31aec7c07d9312981d9..cf6bfaee07c7f81abb3b5b8a56fa526c24c67215 100644
--- a/src/nf_modules/Bowtie/indexing.nf
+++ b/src/nf_modules/bowtie/indexing.nf
@@ -11,7 +11,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..0936530df60624419e4682d686d10ea873f44a32
--- /dev/null
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "bowtie:1.2.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "file://bin/bowtie:1.2.2.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie/1.2.2:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
similarity index 99%
rename from src/nf_modules/Bowtie/mapping_paired.nf
rename to src/nf_modules/bowtie/mapping_paired.nf
index cc9f40b265c61cf0609970fe7501d7267318cf9f..e92cb3d13bf7f05608a6e128201ddc056da3de8c 100644
--- a/src/nf_modules/Bowtie/mapping_paired.nf
+++ b/src/nf_modules/bowtie/mapping_paired.nf
@@ -19,7 +19,6 @@ Channel
 
 process mapping_fastq {
   tag "$pair_id"
-  cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..0936530df60624419e4682d686d10ea873f44a32
--- /dev/null
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "bowtie:1.2.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "file://bin/bowtie:1.2.2.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie/1.2.2:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie/mapping_single.nf b/src/nf_modules/bowtie/mapping_single.nf
similarity index 99%
rename from src/nf_modules/Bowtie/mapping_single.nf
rename to src/nf_modules/bowtie/mapping_single.nf
index ad9754d1545e1154e2fa9bf18bcfde065738723a..490cb1d06bf829e024f4e9d5b7186d071c44e617 100644
--- a/src/nf_modules/Bowtie/mapping_single.nf
+++ b/src/nf_modules/bowtie/mapping_single.nf
@@ -19,7 +19,6 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a30529182addf06c272ca86f9d438d0647b0f49e
--- /dev/null
+++ b/src/nf_modules/bowtie/tests.sh
@@ -0,0 +1,41 @@
+./nextflow src/nf_modules/bowtie/indexing.nf \
+  -c src/nf_modules/bowtie/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/bowtie/mapping_single.nf \
+  -c src/nf_modules/bowtie/mapping_single.config \
+  -profile docker \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/bowtie/mapping_paired.nf \
+  -c src/nf_modules/bowtie/mapping_paired.config \
+  -profile docker \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/bowtie/indexing.nf \
+  -c src/nf_modules/bowtie/indexing.config \
+  -profile singularity \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/bowtie/mapping_single.nf \
+  -c src/nf_modules/bowtie/mapping_single.config \
+  -profile singularity \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/bowtie/mapping_paired.nf \
+  -c src/nf_modules/bowtie/mapping_paired.config \
+  -profile singularity \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..3d0da943a3a54a33c845e8ef042d7c95946cf69f
--- /dev/null
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        container = "bowtie2:2.3.4.1"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "20GB"
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie2/indexing.nf b/src/nf_modules/bowtie2/indexing.nf
similarity index 98%
rename from src/nf_modules/Bowtie2/indexing.nf
rename to src/nf_modules/bowtie2/indexing.nf
index 4f3cde5e990f3528f2f000c8e68131edafdecf97..45318049b076f6dcad4d7ef2335185796a5e7234 100644
--- a/src/nf_modules/Bowtie2/indexing.nf
+++ b/src/nf_modules/bowtie2/indexing.nf
@@ -9,7 +9,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..54410c46293bde9d1ac2a1e75366de06abd317f9
--- /dev/null
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "bowtie2:2.3.4.1"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie2/mapping_paired.nf b/src/nf_modules/bowtie2/mapping_paired.nf
similarity index 99%
rename from src/nf_modules/Bowtie2/mapping_paired.nf
rename to src/nf_modules/bowtie2/mapping_paired.nf
index 7422b143606e720138d07ea3b04fe16d4301c117..dc4667400ec33eed593b1b93decf42994d8777ad 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.nf
+++ b/src/nf_modules/bowtie2/mapping_paired.nf
@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$pair_id"
-  cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..54410c46293bde9d1ac2a1e75366de06abd317f9
--- /dev/null
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "bowtie2:2.3.4.1"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie2/mapping_single.nf b/src/nf_modules/bowtie2/mapping_single.nf
similarity index 99%
rename from src/nf_modules/Bowtie2/mapping_single.nf
rename to src/nf_modules/bowtie2/mapping_single.nf
index 66676991aae710a5263d763dee2ad7dbde6b7a51..1b7954ec174cccd0ad70ee02b79b3fd5b1a91589 100644
--- a/src/nf_modules/Bowtie2/mapping_single.nf
+++ b/src/nf_modules/bowtie2/mapping_single.nf
@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/bowtie2/tests.sh b/src/nf_modules/bowtie2/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bfec0d533a6430fb6cac928fe7350f3fa97a01ae
--- /dev/null
+++ b/src/nf_modules/bowtie2/tests.sh
@@ -0,0 +1,41 @@
+./nextflow src/nf_modules/bowtie2/indexing.nf \
+  -c src/nf_modules/bowtie2/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/bowtie2/mapping_single.nf \
+  -c src/nf_modules/bowtie2/mapping_single.config \
+  -profile docker \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
+  -c src/nf_modules/bowtie2/mapping_paired.config \
+  -profile docker \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/bowtie2/indexing.nf \
+  -c src/nf_modules/bowtie2/indexing.config \
+  -profile singularity \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/bowtie2/mapping_single.nf \
+  -c src/nf_modules/bowtie2/mapping_single.config \
+  -profile singularity \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
+  -c src/nf_modules/bowtie2/mapping_paired.config \
+  -profile singularity \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..f391241a8848c8d91e1b4ce0e4089d27196cc05e
--- /dev/null
+++ b/src/nf_modules/bwa/indexing.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        container = "bwa:0.7.17"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/bwa:0.7.17.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bwa/0.7.17"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/bwa/indexing.nf b/src/nf_modules/bwa/indexing.nf
new file mode 100644
index 0000000000000000000000000000000000000000..09096eeaa0b7e9b77d7078c4edd68734a7d68dbf
--- /dev/null
+++ b/src/nf_modules/bwa/indexing.nf
@@ -0,0 +1,28 @@
+params.fasta = "$baseDir/data/bam/*.fasta"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { fasta_file }
+
+process index_fasta {
+  tag "$fasta_id"
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    set fasta_id, file(fasta) from fasta_file
+
+  output:
+    set fasta_id, "${fasta.baseName}.*" into index_files
+    file "*_bwa_report.txt" into index_files_report
+
+  script:
+"""
+bwa index -p ${fasta.baseName} ${fasta} \
+&> ${fasta.baseName}_bwa_report.txt
+"""
+}
+
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..700b1983129258bd2419287862acce50a8bdf0c4
--- /dev/null
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "bwa:0.7.17"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/bwa:0.7.17.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bwa/0.7.17"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/bwa/mapping_paired.nf b/src/nf_modules/bwa/mapping_paired.nf
new file mode 100644
index 0000000000000000000000000000000000000000..7309c6052fb2e670d29ef51b7b547c59ce092c4a
--- /dev/null
+++ b/src/nf_modules/bwa/mapping_paired.nf
@@ -0,0 +1,37 @@
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.index = "$baseDir/data/index/*.index.*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .groupTuple()
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$reads"
+  publishDir "results/mapping/sam/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+  set index_id, file(index) from index_files.collect()
+
+  output:
+  file "${pair_id}.sam" into sam_files
+  file "${pair_id}_bwa_report.txt" into mapping_repport_files
+
+  script:
+"""
+bwa mem -t ${task.cpus} \
+${index_id} ${reads[0]} ${reads[1]} \
+-o ${pair_id}.sam &> ${pair_id}_bwa_report.txt
+"""
+}
+
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e601d200cd9b642ad7d96ff05be666938e2c6178
--- /dev/null
+++ b/src/nf_modules/bwa/tests.sh
@@ -0,0 +1,42 @@
+./nextflow src/nf_modules/bwa/indexing.nf \
+  -c src/nf_modules/bwa/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+# ./nextflow src/nf_modules/bwa/mapping_single.nf \
+#   -c src/nf_modules/bwa/mapping_single.config \
+#   -profile docker \
+#   --index "results/mapping/index/tiny_v2.index" \
+#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+./nextflow src/nf_modules/bwa/mapping_paired.nf \
+  -c src/nf_modules/bwa/mapping_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/bwa/indexing.nf \
+  -c src/nf_modules/bwa/indexing.config \
+  -profile singularity \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+
+# ./nextflow src/nf_modules/bwa/mapping_single.nf \
+#   -c src/nf_modules/bwa/mapping_single.config \
+#   -profile singularity \
+#   --index "results/mapping/index/tiny_v2.index" \
+#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+./nextflow src/nf_modules/bwa/mapping_paired.nf \
+  -c src/nf_modules/bwa/mapping_paired.config \
+  -profile singularity \
+  --index "results/mapping/index/tiny_v2.*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+fi
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index aa1a372b694db02c9d290a0dccf3c67e14f1c5f7..4f5b5b0484c457c90f21604c7bf6e86c559b1b10 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -3,23 +3,32 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $adaptor_removal {
-        container = "cutadapt:1.14"
+      withName: adaptor_removal {
+        container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
-  sge {
+  psmn {
     process{
-      $adaptor_removal {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: adaptor_removal {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
+        clusterOptions = "-cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index aa1a372b694db02c9d290a0dccf3c67e14f1c5f7..4f5b5b0484c457c90f21604c7bf6e86c559b1b10 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -3,23 +3,32 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $adaptor_removal {
-        container = "cutadapt:1.14"
+      withName: adaptor_removal {
+        container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
-  sge {
+  psmn {
     process{
-      $adaptor_removal {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: adaptor_removal {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
+        clusterOptions = "-cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }
diff --git a/src/nf_modules/cutadapt/tests.sh b/src/nf_modules/cutadapt/tests.sh
index 75089624c4c790df6f4153b2b52048dbfd2d61ad..77712b2083e0ba335a3f0c1944c2e8045b66f4c7 100755
--- a/src/nf_modules/cutadapt/tests.sh
+++ b/src/nf_modules/cutadapt/tests.sh
@@ -1,19 +1,49 @@
 ./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
   -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
 
 ./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
   -c src/nf_modules/cutadapt/adaptor_removal_single.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
 
 ./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
   -c src/nf_modules/cutadapt/trimming_paired.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
 
 ./nextflow src/nf_modules/cutadapt/trimming_single.nf \
   -c src/nf_modules/cutadapt/trimming_single.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
+  -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
+  -c src/nf_modules/cutadapt/adaptor_removal_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
+  -c src/nf_modules/cutadapt/trimming_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_single.nf \
+  -c src/nf_modules/cutadapt/trimming_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index be03e9d728f08bf863f6909e4673f3c0bef810be..023d97588040cac9a2654691f1fad3d85aaeedf3 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -3,23 +3,32 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $trimming {
-        container = "cutadapt:1.14"
+      withName: trimming {
+        container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
-  sge {
+  psmn {
     process{
-      $trimming {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
+        clusterOptions = "-cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index be03e9d728f08bf863f6909e4673f3c0bef810be..023d97588040cac9a2654691f1fad3d85aaeedf3 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -3,23 +3,32 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $trimming {
-        container = "cutadapt:1.14"
+      withName: trimming {
+        container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
-  sge {
+  psmn {
     process{
-      $trimming {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
+        clusterOptions = "-cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
new file mode 100644
index 0000000000000000000000000000000000000000..209ae8c924bf15bd24b010b0b8a3eec393da72e0
--- /dev/null
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -0,0 +1,55 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_bam {
+        container = "sambamba:0.6.7"
+        cpus = 4
+      }
+      withName: bam_to_bigwig {
+        container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+      withName: bam_to_bigwig {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: bam_to_bigwig {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "deeptools/3.0.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.nf b/src/nf_modules/deeptools/bam_to_bigwig.nf
new file mode 100644
index 0000000000000000000000000000000000000000..4c30ee0eed193fba70ea3b236a8bfde800993697
--- /dev/null
+++ b/src/nf_modules/deeptools/bam_to_bigwig.nf
@@ -0,0 +1,49 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+bam_files.into{
+  bam_files_index;
+  bam_files_bigwig
+  }
+
+process index_bam {
+  tag "$file_id"
+
+  input:
+    set file_id, file(bam) from bam_files_index
+
+  output:
+    set file_id, "*.bam*" into indexed_bam_file
+
+  script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
+bam_files_indexed = bam_files_bigwig.join(indexed_bam_file, by: 0)
+
+process bam_to_bigwig {
+  tag "$file_id"
+
+  publishDir "results/mapping/bigwig/", mode: 'copy'
+
+  input:
+    set file_id, file(bam), file(idx) from bam_files_indexed
+
+  output:
+    set file_id, "*.bw" into bw_files
+
+  script:
+"""
+bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} -o ${file_id}.bw
+"""
+}
+
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
new file mode 100644
index 0000000000000000000000000000000000000000..471dde0a4ba33b022b46bd6ee4c3bf246bc0a40d
--- /dev/null
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: compute_matrix {
+        container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_matrix {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: compute_matrix {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "deeptools/3.0.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/deeptools/compute_matrix.nf b/src/nf_modules/deeptools/compute_matrix.nf
new file mode 100644
index 0000000000000000000000000000000000000000..2b6e0e915b00fd1f475818352e11e4ce97225ee0
--- /dev/null
+++ b/src/nf_modules/deeptools/compute_matrix.nf
@@ -0,0 +1,38 @@
+params.bw = "$baseDir/data/bigwig/*.bw"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "bigwig files : ${params.bw}"
+log.info "bed files : ${params.bed}"
+
+Channel
+  .fromPath( params.bw )
+  .ifEmpty { error "Cannot find any bigwig files matching: ${params.bw}" }
+  .set { bw_files }
+
+Channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bed_files }
+
+process compute_matrix {
+  tag "$bed_file_id"
+  publishDir "results/mapping/region_matrix/", mode: 'copy'
+
+  input:
+    file bw from bw_files.collect()
+    set bed_file_id, file(bed) from bed_files.collect()
+
+  output:
+    set bed_file_id, "*.mat.gz" into region_matrix
+
+  script:
+"""
+computeMatrix scale-regions -S ${bw} \
+  -p ${task.cpus} \
+  -R ${bed} \
+  --beforeRegionStartLength 100 \
+  --afterRegionStartLength 100 \
+  -o ${bed_file_id}.mat.gz
+"""
+}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
new file mode 100644
index 0000000000000000000000000000000000000000..306f3a90156b367c72301e0f2973fe8538d80e7d
--- /dev/null
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: plot_profile {
+        container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_matrix {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: plot_profile {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "deeptools/3.0.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/deeptools/plot_profile.nf b/src/nf_modules/deeptools/plot_profile.nf
new file mode 100644
index 0000000000000000000000000000000000000000..dfce4e5504bdd4cede56fa156ffa4fa268a7fede
--- /dev/null
+++ b/src/nf_modules/deeptools/plot_profile.nf
@@ -0,0 +1,36 @@
+params.matrix = "$baseDir/data/region_matrix/*.mat.gz"
+params.title = "plot title"
+
+log.info "matrix files : ${params.matrix}"
+log.info "plot title : ${params.title}"
+
+Channel
+  .fromPath( params.matrix )
+  .ifEmpty { error "Cannot find any matrix files matching: ${params.matrix}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { matrix_files }
+
+process plot_profile {
+  tag "$file_id"
+  publishDir "results/mapping/region_matrix/", mode: 'copy'
+
+  input:
+    set file_id, file(matrix) from matrix_files
+
+  output:
+    set file_id, "*.pdf" into region_matrix
+
+  script:
+/*
+see more option at
+https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html
+*/
+"""
+plotProfile -m ${matrix} \
+  --plotFileFormat=pdf \
+  -out ${file_id}.pdf \
+  --plotType=fill \
+  --perGroup \
+  --plotTitle "${params.title}"
+"""
+}
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4253689a7c94a62feec6be1536f11d394fec909b
--- /dev/null
+++ b/src/nf_modules/deeptools/tests.sh
@@ -0,0 +1,46 @@
+#!/bin/sh
+
+cp data/tiny_dataset/map/tiny_v2.sort.bam \
+  data/tiny_dataset/map/tiny_v2_bis.sort.bam
+
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+  -c src/nf_modules/deeptools/bam_to_bigwig.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+  -c src/nf_modules/deeptools/compute_matrix.config \
+  -profile docker \
+  --bw "results/mapping/bigwig/*.bw" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+  -c src/nf_modules/deeptools/plot_profile.config \
+  -profile docker \
+  --matrix "results/mapping/region_matrix/*.mat.gz" \
+  --title "plot title" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+  -c src/nf_modules/deeptools/bam_to_bigwig.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+  -c src/nf_modules/deeptools/compute_matrix.config \
+  -profile docker \
+  --bw "results/mapping/bigwig/*.bw" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+  -c src/nf_modules/deeptools/plot_profile.config \
+  -profile docker \
+  --matrix "results/mapping/region_matrix/*.mat.gz" \
+  --title "plot title" \
+  -resume
+fi
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..561a3afa0d4aea85daaf76ea2d2bf0f488cce718
--- /dev/null
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastp_fastq {
+        container = "fastp:0.19.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastp_fastq {
+        cpus = 1
+        container = "file://bin/fastp:0.19.7.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastp_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastp/0.19.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/fastp/fastp_paired.nf b/src/nf_modules/fastp/fastp_paired.nf
new file mode 100644
index 0000000000000000000000000000000000000000..88d6710bc93061804681bcceea1bce7ce10cd669
--- /dev/null
+++ b/src/nf_modules/fastp/fastp_paired.nf
@@ -0,0 +1,34 @@
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process fastp_fastq {
+  tag "$pair_id"
+  publishDir "results/fastq/fastp/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+    file "*.{zip,html}" into fastp_report
+    set pair_id, file "*.fastq.gz" fastq_trim_files
+
+  script:
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+--in1 ${reads[0]} \
+--in2 ${reads[1]} \
+--out1 ${pair_id}_R1_trim.fastq.gz \
+--out2 ${pair_id}_R2_trim.fastq.gz \
+--html ${pair_id}.html \
+--report_title ${pair_id}
+"""
+}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..561a3afa0d4aea85daaf76ea2d2bf0f488cce718
--- /dev/null
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastp_fastq {
+        container = "fastp:0.19.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastp_fastq {
+        cpus = 1
+        container = "file://bin/fastp:0.19.7.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastp_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastp/0.19.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/fastp/fastp_single.nf b/src/nf_modules/fastp/fastp_single.nf
new file mode 100644
index 0000000000000000000000000000000000000000..31262172f8e45376b09293b98bdd4fa5403c9b0c
--- /dev/null
+++ b/src/nf_modules/fastp/fastp_single.nf
@@ -0,0 +1,32 @@
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { fastq_files }
+
+process fastp_fastq {
+  tag "$file_id"
+  publishDir "results/fastq/fastp/", mode: 'copy'
+
+  input:
+  set file_id, file(reads) from fastq_files
+
+  output:
+    file "*.{zip,html}" into fastp_report
+    set file_id, file "*.fastq.gz" fastq_trim_files
+
+  script:
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--in1 ${reads} \
+--out1 ${file_id}_R1_trim.fastq.gz \
+--html ${file_id}.html \
+--report_title ${file_id}
+"""
+}
diff --git a/src/nf_modules/fastp/tests.sh b/src/nf_modules/fastp/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fae4f08a92c56752b4d467b5c31aca629eb2aac3
--- /dev/null
+++ b/src/nf_modules/fastp/tests.sh
@@ -0,0 +1,25 @@
+./nextflow src/nf_modules/fastp/fastp_paired.nf \
+  -c src/nf_modules/fastp/fastp_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastp/fastp_single.nf \
+  -c src/nf_modules/fastp/fastp_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/fastp/fastp_paired.nf \
+  -c src/nf_modules/fastp/fastp_paired.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastp/fastp_single.nf \
+  -c src/nf_modules/fastp/fastp_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..9e75046a9c9a7f0d1e9e6f62d266a3c857ba67c3
--- /dev/null
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "fastqc:0.11.5"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        cpus = 1
+        container = "file://bin/fastqc:0.11.5.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastqc_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastqc/0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/FastQC/fastqc_paired.nf b/src/nf_modules/fastqc/fastqc_paired.nf
similarity index 100%
rename from src/nf_modules/FastQC/fastqc_paired.nf
rename to src/nf_modules/fastqc/fastqc_paired.nf
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..9e75046a9c9a7f0d1e9e6f62d266a3c857ba67c3
--- /dev/null
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "fastqc:0.11.5"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        cpus = 1
+        container = "file://bin/fastqc:0.11.5.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastqc_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastqc/0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/FastQC/fastqc_single.nf b/src/nf_modules/fastqc/fastqc_single.nf
similarity index 98%
rename from src/nf_modules/FastQC/fastqc_single.nf
rename to src/nf_modules/fastqc/fastqc_single.nf
index 459841651ec85102f38a980bc621d0ca1c8626bb..ab7e22aade6df50ad6a87f574c9d1eb57cd35c02 100644
--- a/src/nf_modules/FastQC/fastqc_single.nf
+++ b/src/nf_modules/fastqc/fastqc_single.nf
@@ -11,7 +11,6 @@ Channel
 process fastqc_fastq {
   tag "$file_id"
   publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
 
   input:
   set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/fastqc/tests.sh b/src/nf_modules/fastqc/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7002e71d6396d407f5ba9f37864ccdbf661597f3
--- /dev/null
+++ b/src/nf_modules/fastqc/tests.sh
@@ -0,0 +1,25 @@
+./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
+  -c src/nf_modules/fastqc/fastqc_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastqc/fastqc_single.nf \
+  -c src/nf_modules/fastqc/fastqc_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
+  -c src/nf_modules/fastqc/fastqc_paired.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastqc/fastqc_single.nf \
+  -c src/nf_modules/fastqc/fastqc_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
new file mode 100644
index 0000000000000000000000000000000000000000..9e0a4e579b78773190df476f902bc294243e4d6b
--- /dev/null
+++ b/src/nf_modules/htseq/htseq.config
@@ -0,0 +1,49 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: sort_bam {
+        container = "samtools:1.7"
+        cpus = 1
+      }
+      withName: counting {
+        container = "htseq:0.8.0"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/htseq:0.8.0.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: sort_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "htseq/0.8.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/HTSeq/htseq.nf b/src/nf_modules/htseq/htseq.nf
similarity index 100%
rename from src/nf_modules/HTSeq/htseq.nf
rename to src/nf_modules/htseq/htseq.nf
diff --git a/src/nf_modules/htseq/tests.sh b/src/nf_modules/htseq/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..904b42b3476e4daf3e97b6e52f435a507c033cd0
--- /dev/null
+++ b/src/nf_modules/htseq/tests.sh
@@ -0,0 +1,15 @@
+./nextflow src/nf_modules/htseq/htseq.nf \
+  -c src/nf_modules/htseq/htseq.config \
+  -profile docker \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/htseq/htseq.nf \
+  -c src/nf_modules/htseq/htseq.config \
+  -profile docker \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..49bc912aa8f753770159749d8b50608e7888b267
--- /dev/null
+++ b/src/nf_modules/kallisto/indexing.config
@@ -0,0 +1,38 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+
diff --git a/src/nf_modules/Kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
similarity index 98%
rename from src/nf_modules/Kallisto/indexing.nf
rename to src/nf_modules/kallisto/indexing.nf
index 9e38260f87e9bfa4384b69ef440c73acb6feba05..ea153569693b5dd057727a072d14dadd0ce77bf5 100644
--- a/src/nf_modules/Kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -9,7 +9,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..ef4991498ca24bbb1d8ff14b28c93b2efbaa0bf4
--- /dev/null
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -0,0 +1,38 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+
diff --git a/src/nf_modules/Kallisto/mapping_paired.nf b/src/nf_modules/kallisto/mapping_paired.nf
similarity index 98%
rename from src/nf_modules/Kallisto/mapping_paired.nf
rename to src/nf_modules/kallisto/mapping_paired.nf
index 4f4ad3d167292dcf9919506f89103dbbbab7f709..455e70cd4030a28e9fe3fcaccadc92e915c75859 100644
--- a/src/nf_modules/Kallisto/mapping_paired.nf
+++ b/src/nf_modules/kallisto/mapping_paired.nf
@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$reads"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..ef4991498ca24bbb1d8ff14b28c93b2efbaa0bf4
--- /dev/null
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -0,0 +1,38 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+
diff --git a/src/nf_modules/Kallisto/mapping_single.nf b/src/nf_modules/kallisto/mapping_single.nf
similarity index 99%
rename from src/nf_modules/Kallisto/mapping_single.nf
rename to src/nf_modules/kallisto/mapping_single.nf
index 97861e76faad7a266b279bb6fe8ac77964c94284..95bed86418491de0f8038a23c14c6b75eb973d55 100644
--- a/src/nf_modules/Kallisto/mapping_single.nf
+++ b/src/nf_modules/kallisto/mapping_single.nf
@@ -20,7 +20,6 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/kallisto/tests.sh b/src/nf_modules/kallisto/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f8816f0ab6ea505a9c0cb22331107d612f6fadf4
--- /dev/null
+++ b/src/nf_modules/kallisto/tests.sh
@@ -0,0 +1,41 @@
+./nextflow src/nf_modules/kallisto/indexing.nf \
+  -c src/nf_modules/kallisto/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_single.nf \
+  -c src/nf_modules/kallisto/mapping_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_paired.nf \
+  -c src/nf_modules/kallisto/mapping_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/kallisto/indexing.nf \
+  -c src/nf_modules/kallisto/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_single.nf \
+  -c src/nf_modules/kallisto/mapping_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_paired.nf \
+  -c src/nf_modules/kallisto/mapping_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
new file mode 100644
index 0000000000000000000000000000000000000000..8462ab8651cbbeb0b23d3cc213d6f9142be5e5c0
--- /dev/null
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: peak_calling {
+        container = "macs2:2.1.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: peak_calling {
+        container = "file://bin/macs2:2.1.2.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: peak_calling {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "macs2/2.1.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/macs2/peak_calling.nf b/src/nf_modules/macs2/peak_calling.nf
new file mode 100644
index 0000000000000000000000000000000000000000..12398f2e92e48f8df7936efe62d4778c8112cdfd
--- /dev/null
+++ b/src/nf_modules/macs2/peak_calling.nf
@@ -0,0 +1,52 @@
+params.genome_size = "hs"
+params.control_tag = "control"
+log.info "bam files : ${params.bam}"
+log.info "genome size : ${params.genome_size}"
+log.info "control tag : ${params.control_tag}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+/* split bam Channel into control and ip if "control" keyword is detected*/
+bam_files_control = Channel.create()
+bam_files_ip = Channel.create()
+bam_files.choice(
+  bam_files_control,
+  bam_files_ip ) { a -> a[0] =~ /.*${params.control_tag}.*/ ? 0 : 1 }
+
+process peak_calling {
+  tag "${file_id}"
+  publishDir "results/peak_calling/${file_id}", mode: 'copy'
+
+  input:
+    set file_id, file(file_ip) from bam_files_ip
+    set file_id_control, file(file_control) from bam_files_control
+      .ifEmpty {
+        error "Cannot find any bam files matching: ${params.control_tag}"
+      }
+      .collect()
+
+  output:
+    file "*" into peak_output
+    file "*_report.txt" into peak_calling_report
+
+  script:
+/* remove --nomodel option for real dataset */
+"""
+macs2 callpeak \
+  --nomodel \
+  --treatment ${file_ip} \
+  --control ${file_control} \
+  --name ${file_id} \
+  --gsize ${params.genome_size} 2> \
+${file_ip}_macs2_report.txt
+
+if grep -q "ERROR" ${file_ip}_macs2_report.txt; then
+  echo "MACS2 error"
+  exit 1
+fi
+"""
+}
diff --git a/src/nf_modules/macs2/tests.sh b/src/nf_modules/macs2/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fc73ce29a9e9aed5ee83ba0e171e49059185bc5c
--- /dev/null
+++ b/src/nf_modules/macs2/tests.sh
@@ -0,0 +1,18 @@
+cp data/tiny_dataset/map/tiny_v2.bam data/tiny_dataset/map/tiny_v2_control.bam
+./nextflow src/nf_modules/macs2/peak_calling.nf \
+  -c src/nf_modules/macs2/peak_calling.config \
+  -profile docker \
+  -resume \
+  --bam "data/tiny_dataset/map/tiny_v2*.bam" \
+  --genome_size 129984 \
+  --control_tag "control"
+
+if [ -x "$(command -v singularity)" ]; then
+  ./nextflow src/nf_modules/macs2/peak_calling.nf \
+    -c src/nf_modules/macs2/peak_calling.config \
+    -profile singularity \
+    -resume \
+    --bam "data/tiny_dataset/map/tiny_v2*.bam" \
+    --genome_size 129984 \
+    --control_tag "control"
+fi
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..aaa32da19c1ef5b6b3a0108cf97a54e7ac191e71
--- /dev/null
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -0,0 +1,59 @@
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "fastqc:0.11.5"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "multiqc:1.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "file://bin/fastqc:0.11.5.sif"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "file://bin/multiqc:1.7.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastqc_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastqc/0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1.70
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: multiqc {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "multiqc/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1.70
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+
diff --git a/src/nf_modules/MultiQC/multiqc_paired.nf b/src/nf_modules/multiqc/multiqc_paired.nf
similarity index 100%
rename from src/nf_modules/MultiQC/multiqc_paired.nf
rename to src/nf_modules/multiqc/multiqc_paired.nf
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..bdf605046e60e22feb08e8a332a69c5834332570
--- /dev/null
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -0,0 +1,57 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "fastqc:0.11.5"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "multiqc:1.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "file://bin/fastqc:0.11.5.sif"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "file://bin/multiqc:1.7.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastqc_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastqc/0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1.70
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: multiqc {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "multiqc/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1.70
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/MultiQC/multiqc_single.nf b/src/nf_modules/multiqc/multiqc_single.nf
similarity index 100%
rename from src/nf_modules/MultiQC/multiqc_single.nf
rename to src/nf_modules/multiqc/multiqc_single.nf
diff --git a/src/nf_modules/multiqc/tests.sh b/src/nf_modules/multiqc/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0ba607642695fc8a0e30c67f3658cef0da020378
--- /dev/null
+++ b/src/nf_modules/multiqc/tests.sh
@@ -0,0 +1,25 @@
+./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
+  -c src/nf_modules/multiqc/multiqc_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/multiqc/multiqc_single.nf \
+  -c src/nf_modules/multiqc/multiqc_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
+  -c src/nf_modules/multiqc/multiqc_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/multiqc/multiqc_single.nf \
+  -c src/nf_modules/multiqc/multiqc_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..d21fe81da5cee0f002abba1993293c789cc50f86
--- /dev/null
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -0,0 +1,71 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: compute_mappability {
+        container = "music:6613c53"
+        cpus = 1
+      }
+      withName: music_preprocessing {
+        container = "music:6613c53"
+        cpus = 1
+      }
+      withName: music_computation {
+        container = "music:6613c53"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_mappability {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
+      }
+      withName: music_preprocessing {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
+      }
+      withName: music_computation {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: compute_mappability {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "music/6613c53"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+      withName: music_preprocessing {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "music/6613c53"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+      withName: music_computation {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "music/6613c53"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/MUSIC/peak_calling_single.nf b/src/nf_modules/music/peak_calling_single.nf
similarity index 100%
rename from src/nf_modules/MUSIC/peak_calling_single.nf
rename to src/nf_modules/music/peak_calling_single.nf
diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4169c449d5706e01a28c443247bf04c2a39fe40d
--- /dev/null
+++ b/src/nf_modules/music/tests.sh
@@ -0,0 +1,20 @@
+cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control.sort.bam
+./nextflow src/nf_modules/music/peak_calling_single.nf \
+  -c src/nf_modules/music/peak_calling_single.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --bam "data/tiny_dataset/map/*.sort.bam" \
+  --index "data/tiny_dataset/map/*.sort.bam.bai*" \
+  --read_size 50 --frag_size 300 \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/music/peak_calling_single.nf \
+  -c src/nf_modules/music/peak_calling_single.config \
+  -profile singularity \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --bam "data/tiny_dataset/map/*.sort.bam" \
+  --index "data/tiny_dataset/map/*.sort.bam.bai*" \
+  --read_size 50 --frag_size 300 \
+  -resume
+fi
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..aeea35fe8614f890077faaba3fb65bef3cc216bb
--- /dev/null
+++ b/src/nf_modules/rsem/indexing.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "rsem/1.3.0:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/RSEM/indexing.nf b/src/nf_modules/rsem/indexing.nf
similarity index 99%
rename from src/nf_modules/RSEM/indexing.nf
rename to src/nf_modules/rsem/indexing.nf
index 0f5473ac900f1d7c99975db7467abed466b98abb..4b95622aaa31f5eece4390f3f09418750e44570c 100644
--- a/src/nf_modules/RSEM/indexing.nf
+++ b/src/nf_modules/rsem/indexing.nf
@@ -14,7 +14,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..812167ed15e95cea57dbc0e7d4540df942bcc733
--- /dev/null
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "rsem/1.3.0:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/RSEM/quantification_paired.nf b/src/nf_modules/rsem/quantification_paired.nf
similarity index 99%
rename from src/nf_modules/RSEM/quantification_paired.nf
rename to src/nf_modules/rsem/quantification_paired.nf
index a22950fd2b4a0548ea7a45bc0a0965992246047f..c9e23ac8d19e510eee63823069dcb5bc86a38c9b 100644
--- a/src/nf_modules/RSEM/quantification_paired.nf
+++ b/src/nf_modules/rsem/quantification_paired.nf
@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$pair_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..812167ed15e95cea57dbc0e7d4540df942bcc733
--- /dev/null
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "rsem/1.3.0:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/RSEM/quantification_single.nf b/src/nf_modules/rsem/quantification_single.nf
similarity index 96%
rename from src/nf_modules/RSEM/quantification_single.nf
rename to src/nf_modules/rsem/quantification_single.nf
index d52b7f446049abac081b5a17f2202909f070e600..bacba6b33ab974f4390cdcff141ad4222be5b1db 100644
--- a/src/nf_modules/RSEM/quantification_single.nf
+++ b/src/nf_modules/rsem/quantification_single.nf
@@ -20,12 +20,11 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
   set file_id, file(reads) from fastq_files
-  file index from index_files.toList()
+  file index from index_files.collect()
 
   output:
   file "*" into count_files
@@ -38,7 +37,6 @@ process mapping_fastq {
     }
   }
 """
-ls -l
 rsem-calculate-expression --bowtie2 \
 --bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
 --bowtie2-sensitivity-level "very_sensitive" \
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e4cd27267371e378d4c47454f9344298cdde4566
--- /dev/null
+++ b/src/nf_modules/rsem/tests.sh
@@ -0,0 +1,44 @@
+./nextflow src/nf_modules/rsem/indexing.nf \
+  -c src/nf_modules/rsem/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --annotation "data/tiny_dataset/annot/tiny.gff" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_single.nf \
+  -c src/nf_modules/rsem/quantification_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_paired.nf \
+  -c src/nf_modules/rsem/quantification_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/rsem/indexing.nf \
+  -c src/nf_modules/rsem/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --annotation "data/tiny_dataset/annot/tiny.gff" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_single.nf \
+  -c src/nf_modules/rsem/quantification_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_paired.nf \
+  -c src/nf_modules/rsem/quantification_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..8cbbd24b2129f2ec3a52acaedba253f17f34160c
--- /dev/null
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_bam {
+        container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/sambamba/index_bams.nf b/src/nf_modules/sambamba/index_bams.nf
new file mode 100644
index 0000000000000000000000000000000000000000..3ea36df4a3e512fba7b577b4b2c6916a4e0bb940
--- /dev/null
+++ b/src/nf_modules/sambamba/index_bams.nf
@@ -0,0 +1,25 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process index_bam {
+  tag "$file_id"
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*.bam*" into indexed_bam_file
+
+  script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..11811d97cfa36527c48414459c4be7d3cdf20d82
--- /dev/null
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: sort_bam {
+        container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: sort_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 4
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/sambamba/sort_bams.nf b/src/nf_modules/sambamba/sort_bams.nf
new file mode 100644
index 0000000000000000000000000000000000000000..ac610cdca146693df69d8b765928d406b36652b6
--- /dev/null
+++ b/src/nf_modules/sambamba/sort_bams.nf
@@ -0,0 +1,26 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process sort_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_sorted.bam" into sorted_bam_files
+
+  script:
+"""
+sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+"""
+}
+
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..6df50fc7397bf2e76ef75531f77c361b98435dc9
--- /dev/null
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: split_bam {
+        container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: split_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/sambamba/split_bams.nf b/src/nf_modules/sambamba/split_bams.nf
new file mode 100644
index 0000000000000000000000000000000000000000..ba64d2e2b77eb3a9b24ec1355c2b3a68b95c7a4d
--- /dev/null
+++ b/src/nf_modules/sambamba/split_bams.nf
@@ -0,0 +1,27 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process split_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_forward.bam*" into forward_bam_files
+    set file_id, "*_reverse.bam*" into reverse_bam_files
+  script:
+"""
+sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
+sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
+"""
+}
+
diff --git a/src/nf_modules/sambamba/tests.sh b/src/nf_modules/sambamba/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..256df65f9ed23efac640aea6548f15397479ca60
--- /dev/null
+++ b/src/nf_modules/sambamba/tests.sh
@@ -0,0 +1,37 @@
+./nextflow src/nf_modules/sambamba/sort_bams.nf \
+  -c src/nf_modules/sambamba/sort_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/index_bams.nf \
+  -c src/nf_modules/sambamba/index_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/split_bams.nf \
+  -c src/nf_modules/sambamba/split_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/sambamba/sort_bams.nf \
+  -c src/nf_modules/sambamba/sort_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/index_bams.nf \
+  -c src/nf_modules/sambamba/index_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/split_bams.nf \
+  -c src/nf_modules/sambamba/split_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
new file mode 100644
index 0000000000000000000000000000000000000000..75efda223362e7f0d6594bc4e3c339f2b3c9857f
--- /dev/null
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: dedup_sam {
+        container = "samblaster:0.1.24"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: dedup_sam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samblaster/0.1.24"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/samblaster/dedup_sams.nf b/src/nf_modules/samblaster/dedup_sams.nf
new file mode 100644
index 0000000000000000000000000000000000000000..bcfd829c6bba1c119ea71e34ef5d148c693e4fcf
--- /dev/null
+++ b/src/nf_modules/samblaster/dedup_sams.nf
@@ -0,0 +1,27 @@
+params.sam = "$baseDir/data/sam/*.bam"
+
+log.info "bam files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process dedup_sam {
+  tag "$file_id"
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_dedup.bam*" into dedup_bam_files
+  script:
+"""
+samtools view -h ${bam} | \
+samblaster --addMateTags 2> /dev/null | \
+samtools view -Sb - > ${file_id}_dedup.bam
+"""
+}
+
+
diff --git a/src/nf_modules/samblaster/tests.sh b/src/nf_modules/samblaster/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..10ad93d7841ba4b708664803c0ca1299cc34ee19
--- /dev/null
+++ b/src/nf_modules/samblaster/tests.sh
@@ -0,0 +1,13 @@
+./nextflow src/nf_modules/samblaster/dedup_sams.nf \
+  -c src/nf_modules/samblaster/dedup_sams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/samblaster/dedup_sams.nf \
+  -c src/nf_modules/samblaster/dedup_sams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..87d99007b08d77f57d5edf576ff288da1f78ec99
--- /dev/null
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: filter_bam {
+        container = "samtools:1.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: filter_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: filter_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/SAMtools/filter_bams.nf b/src/nf_modules/samtools/filter_bams.nf
similarity index 98%
rename from src/nf_modules/SAMtools/filter_bams.nf
rename to src/nf_modules/samtools/filter_bams.nf
index 0812a19b227049fd05b54f46cbc30b246da73127..6e81b758dede1f317d981409f7c85571ede55b06 100644
--- a/src/nf_modules/SAMtools/filter_bams.nf
+++ b/src/nf_modules/samtools/filter_bams.nf
@@ -16,7 +16,6 @@ Channel
 
 process filter_bam {
   tag "$file_id"
-  cpus 4
 
   input:
     set file_id, file(bam) from bam_files
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..762773b473e61d7d863c344dad284b38c50f1f31
--- /dev/null
+++ b/src/nf_modules/samtools/index_bams.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_bam {
+        container = "samtools:1.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/SAMtools/index_bams.nf b/src/nf_modules/samtools/index_bams.nf
similarity index 100%
rename from src/nf_modules/SAMtools/index_bams.nf
rename to src/nf_modules/samtools/index_bams.nf
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..63c23123cb2798e306d1163bd3999c0922726f04
--- /dev/null
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -0,0 +1,36 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: sort_bam {
+        container = "samtools:1.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: sort_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/SAMtools/sort_bams.nf b/src/nf_modules/samtools/sort_bams.nf
similarity index 98%
rename from src/nf_modules/SAMtools/sort_bams.nf
rename to src/nf_modules/samtools/sort_bams.nf
index ab5c7e5140989b83eebd25f7b4dbb206520416b6..db1b30d1d6d59ae74535267815f6f887e2b267dd 100644
--- a/src/nf_modules/SAMtools/sort_bams.nf
+++ b/src/nf_modules/samtools/sort_bams.nf
@@ -10,7 +10,6 @@ Channel
 
 process sort_bam {
   tag "$file_id"
-  cpus 4
 
   input:
     set file_id, file(bam) from bam_files
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
new file mode 100644
index 0000000000000000000000000000000000000000..de924648525a4b23e4717102f8c566338d895a25
--- /dev/null
+++ b/src/nf_modules/samtools/split_bams.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: split_bam {
+        container = "samtools:1.7"
+        cpus = 2
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 2
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: split_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/SAMtools/split_bams.nf b/src/nf_modules/samtools/split_bams.nf
similarity index 98%
rename from src/nf_modules/SAMtools/split_bams.nf
rename to src/nf_modules/samtools/split_bams.nf
index f8ba6a50c7d7aecfb7c9c7b0fff8d4436cf055a4..0d02a5d170893a88625a0885ffed16e1adbef35c 100644
--- a/src/nf_modules/SAMtools/split_bams.nf
+++ b/src/nf_modules/samtools/split_bams.nf
@@ -10,7 +10,6 @@ Channel
 
 process split_bam {
   tag "$file_id"
-  cpus 2
 
   input:
     set file_id, file(bam) from bam_files
diff --git a/src/nf_modules/samtools/tests.sh b/src/nf_modules/samtools/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..256fa058beeaf3464391f4e974a2b4a2ef499b0c
--- /dev/null
+++ b/src/nf_modules/samtools/tests.sh
@@ -0,0 +1,51 @@
+./nextflow src/nf_modules/samtools/sort_bams.nf \
+  -c src/nf_modules/samtools/sort_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/index_bams.nf \
+  -c src/nf_modules/samtools/index_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/split_bams.nf \
+  -c src/nf_modules/samtools/split_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/filter_bams.nf \
+  -c src/nf_modules/samtools/filter_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  --bed "data/tiny_dataset/OLD/2genes.bed" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/samtools/sort_bams.nf \
+  -c src/nf_modules/samtools/sort_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/index_bams.nf \
+  -c src/nf_modules/samtools/index_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/split_bams.nf \
+  -c src/nf_modules/samtools/split_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/filter_bams.nf \
+  -c src/nf_modules/samtools/filter_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  --bed "data/tiny_dataset/OLD/2genes.bed" \
+  -resume
+fi
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
new file mode 100644
index 0000000000000000000000000000000000000000..2fc5039ff3fae99cbbc5bf5af69456834188d4b1
--- /dev/null
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -0,0 +1,35 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastq_dump {
+        container = "sratoolkit:2.8.2"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 1
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastq_dump {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sratoolkit/2.8.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.nf b/src/nf_modules/sratoolkit/fastqdump.nf
similarity index 100%
rename from src/nf_modules/SRAtoolkit/fastqdump.nf
rename to src/nf_modules/sratoolkit/fastqdump.nf
diff --git a/src/nf_modules/SRAtoolkit/list-srr.txt b/src/nf_modules/sratoolkit/list-srr.txt
similarity index 100%
rename from src/nf_modules/SRAtoolkit/list-srr.txt
rename to src/nf_modules/sratoolkit/list-srr.txt
diff --git a/src/nf_modules/sratoolkit/tests.sh b/src/nf_modules/sratoolkit/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1747137d454630bffa8538efc3009469f271b50c
--- /dev/null
+++ b/src/nf_modules/sratoolkit/tests.sh
@@ -0,0 +1,13 @@
+./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
+  -c src/nf_modules/sratoolkit/fastqdump.config \
+  -profile docker \
+  --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
+  -c src/nf_modules/sratoolkit/fastqdump.config \
+  -profile docker \
+  --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
+  -resume
+fi
diff --git a/src/nf_modules/urqt/tests.sh b/src/nf_modules/urqt/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9992c67490ce65df42471a73d5c36bb0b708763e
--- /dev/null
+++ b/src/nf_modules/urqt/tests.sh
@@ -0,0 +1,25 @@
+./nextflow src/nf_modules/urqt/trimming_paired.nf \
+  -c src/nf_modules/urqt/trimming_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/urqt/trimming_single.nf \
+  -c src/nf_modules/urqt/trimming_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/urqt/trimming_single.nf \
+  -c src/nf_modules/urqt/trimming_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/urqt/trimming_single.nf \
+  -c src/nf_modules/urqt/trimming_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+fi
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..f0b084b8e3048736787d405678edf1e7db7a2577
--- /dev/null
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -0,0 +1,37 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: trimming {
+        cpus = 4
+        container = "urqt:d62c1f8"
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        cpus = 4
+        container = "file://bin/urqt:d62c1f8.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "urqt/d62c1f8"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        memory = "5GB"
+        cpus = 16
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
diff --git a/src/nf_modules/UrQt/trimming_paired.nf b/src/nf_modules/urqt/trimming_paired.nf
similarity index 98%
rename from src/nf_modules/UrQt/trimming_paired.nf
rename to src/nf_modules/urqt/trimming_paired.nf
index 7720b12fa2739bda9e0b27e1968102c25298fbf1..f15efac0c306cd09280b791035fccfc3efc6f039 100644
--- a/src/nf_modules/UrQt/trimming_paired.nf
+++ b/src/nf_modules/urqt/trimming_paired.nf
@@ -7,7 +7,6 @@ Channel
 
 process trimming {
   tag "${reads}"
-  cpus 4
   publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..02788fcb559b010c2856920828b0f651de215d11
--- /dev/null
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -0,0 +1,37 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: trimming {
+        container = "urqt:d62c1f8"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        container = "file://bin/urqt:d62c1f8.sif"
+        cpus = 4
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "urqt/d62c1f8"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "5GB"
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
diff --git a/src/nf_modules/UrQt/trimming_single.nf b/src/nf_modules/urqt/trimming_single.nf
similarity index 98%
rename from src/nf_modules/UrQt/trimming_single.nf
rename to src/nf_modules/urqt/trimming_single.nf
index 5eb1e84c57b26417e6794af8bbbe03dc5377c7c7..4116a69a7af5164ea59aa918fd314238f5068b77 100644
--- a/src/nf_modules/UrQt/trimming_single.nf
+++ b/src/nf_modules/urqt/trimming_single.nf
@@ -10,7 +10,7 @@ Channel
 
 process trimming {
   tag "$file_id"
-  cpus 4
+  echo true
 
   input:
   set file_id, file(reads) from fastq_files
diff --git a/src/psmn_modules b/src/psmn_modules
new file mode 160000
index 0000000000000000000000000000000000000000..c39bdc845287ae2ef53f320f56b6f70b24ff30af
--- /dev/null
+++ b/src/psmn_modules
@@ -0,0 +1 @@
+Subproject commit c39bdc845287ae2ef53f320f56b6f70b24ff30af
diff --git a/src/sge_modules b/src/sge_modules
deleted file mode 160000
index 1d6cfb91449b187b05a3a78df9a06ff3baaf5558..0000000000000000000000000000000000000000
--- a/src/sge_modules
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 1d6cfb91449b187b05a3a78df9a06ff3baaf5558
diff --git a/src/singularity_modules/bcftools/1.7/bcftools.def b/src/singularity_modules/bcftools/1.7/bcftools.def
new file mode 100644
index 0000000000000000000000000000000000000000..1d3535653014ed88d79ad49e4b23a03412013446
--- /dev/null
+++ b/src/singularity_modules/bcftools/1.7/bcftools.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BCFTOOLS_VERSION=1.7
+PACKAGES=bcftools=${BCFTOOLS_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export BCFTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/bcftools/1.7/build.sh b/src/singularity_modules/bcftools/1.7/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bee821bdc4f9791ea199ffe11a72643f745ce26d
--- /dev/null
+++ b/src/singularity_modules/bcftools/1.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bcftools:1.7.sif src/singularity_modules/bcftools/1.7/bcftools.def && \
+singularity sign bin/bcftools:1.7.sif
diff --git a/src/singularity_modules/bedtools/2.25.0/bedtools.def b/src/singularity_modules/bedtools/2.25.0/bedtools.def
new file mode 100644
index 0000000000000000000000000000000000000000..0ca0f9ef362991a45cc0bf101ed82d81de356d60
--- /dev/null
+++ b/src/singularity_modules/bedtools/2.25.0/bedtools.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:16.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BEDTOOLS_VERSION=2.25.0
+PACKAGES=bedtools=${BEDTOOLS_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export BEDTOOLS_VERSION=2.25.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/bedtools/2.25.0/build.sh b/src/singularity_modules/bedtools/2.25.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..60644b467833cde7327376293de5700d95358081
--- /dev/null
+++ b/src/singularity_modules/bedtools/2.25.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bedtools:2.25.0.sif src/singularity_modules/bedtools/2.25.0/bedtools.def && \
+singularity sign bin/bedtools:2.25.0.sif
diff --git a/src/singularity_modules/bioawk/1.0/bioawk.def b/src/singularity_modules/bioawk/1.0/bioawk.def
new file mode 100644
index 0000000000000000000000000000000000000000..a5678b646c7cee4bb058c1bd316c1e35be763983
--- /dev/null
+++ b/src/singularity_modules/bioawk/1.0/bioawk.def
@@ -0,0 +1,31 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BIOAWK_VERSION=1.0
+PACKAGES="git \
+   build-essential \
+   ca-certificates \
+   zlib1g-dev \
+   byacc"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/lh3/bioawk.git && \
+  cd bioawk && \
+  git checkout tags/v${BIOAWK_VERSION} && \
+  make && \
+  cd .. && \
+  mv bioawk/bioawk /usr/bin/ && \
+  rm -Rf bioawk
+
+%environment
+export BIOAWK_VERSION=1.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/bioawk/1.0/build.sh b/src/singularity_modules/bioawk/1.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3f8adc0419f1556b31a349761e8b6bd995181ea4
--- /dev/null
+++ b/src/singularity_modules/bioawk/1.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bioawk:1.0.sif src/singularity_modules/bioawk/1.0/bioawk.def && \
+singularity sign bin/bioawk:1.0.sif
diff --git a/src/singularity_modules/bowtie/1.2.2/bowtie.def b/src/singularity_modules/bowtie/1.2.2/bowtie.def
new file mode 100644
index 0000000000000000000000000000000000000000..79da11614f57813f69f3ac863606e2c5fa69efc8
--- /dev/null
+++ b/src/singularity_modules/bowtie/1.2.2/bowtie.def
@@ -0,0 +1,22 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BOWTIE_VERSION=1.2.2
+SAMTOOLS_VERSION=1.7
+PACKAGES="bowtie=${BOWTIE_VERSION}* \
+samtools=${SAMTOOLS_VERSION}*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export BOWTIE_VERSION=1.2.2
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/bowtie/1.2.2/build.sh b/src/singularity_modules/bowtie/1.2.2/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3470fca0a1764c0fb4eda3f57097328563c05dc4
--- /dev/null
+++ b/src/singularity_modules/bowtie/1.2.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/bowtie/1.2.2/bowtie.def && \
+singularity sign bin/bowtie:1.2.2.sif
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
new file mode 100644
index 0000000000000000000000000000000000000000..73a177e449b3e3acb2330909edfb055cac9cb709
--- /dev/null
+++ b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
@@ -0,0 +1,23 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BOWTIE2_VERSION=2.3.4.1
+SAMTOOLS_VERSION=1.7
+PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
+samtools=${SAMTOOLS_VERSION}* \
+perl=5.26.1*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export BOWTIE2_VERSION=2.3.4.1
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/build.sh b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f9f58ae6044cf3241d16974e06a19678ccaad710
--- /dev/null
+++ b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
+singularity sign bin/bowtie2:2.3.4.1.sif
diff --git a/src/singularity_modules/bwa/0.7.17/build.sh b/src/singularity_modules/bwa/0.7.17/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a340c5f8698caf67031934f912fad2cb45d22578
--- /dev/null
+++ b/src/singularity_modules/bwa/0.7.17/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/bwa/0.7.17/bwa.def && \
+singularity sign bin/bwa:0.7.17.sif
diff --git a/src/singularity_modules/bwa/0.7.17/bwa.def b/src/singularity_modules/bwa/0.7.17/bwa.def
new file mode 100644
index 0000000000000000000000000000000000000000..b2c8b22fd8953f61d7921bc9335dca0f6e11e55e
--- /dev/null
+++ b/src/singularity_modules/bwa/0.7.17/bwa.def
@@ -0,0 +1,46 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BWA_VERSION=0.7.17
+SAMBLASTER_VERSION=0.1.24
+
+PACKAGES=curl="7.58.0* \
+ca-certificates=20180409 \
+build-essential=12.4* \
+zlib1g-dev=1:1.2.11*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+
+curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
+tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
+cd bwa-${BWA_VERSION}/ && \
+make && \
+cp bwa /usr/bin && \
+cd .. && \
+rm -R bwa-${BWA_VERSION}/
+
+curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
+
+%environment
+export BWA_VERSION=0.7.17
+export SAMBLASTER_VERSION=0.1.24
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/canu/1.6/build.sh b/src/singularity_modules/canu/1.6/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..591cb660b7b84e69eb4ec1acbc3ba04de0d2baf4
--- /dev/null
+++ b/src/singularity_modules/canu/1.6/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/canu:1.6.sif src/singularity_modules/canu/1.6/canu.def && \
+singularity sign bin/canu:1.6.sif
diff --git a/src/singularity_modules/canu/1.6/canu.def b/src/singularity_modules/canu/1.6/canu.def
new file mode 100644
index 0000000000000000000000000000000000000000..c9d0a4ece7945509d00ff199cff6abffc613c489
--- /dev/null
+++ b/src/singularity_modules/canu/1.6/canu.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CANU_VERSION=1.6
+PACKAGES=canu=${CANU_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export CANU_VERSION=1.6
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/cutadapt/1.14/build.sh b/src/singularity_modules/cutadapt/1.14/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5327f7c468b5e3a800f42d46e89ae6f1bcafa2c4
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.14/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/cutadapt:1.14.sif src/singularity_modules/cutadapt/1.14/cutadapt.def && \
+singularity sign bin/cutadapt:1.14.sif
diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt.def b/src/singularity_modules/cutadapt/1.14/cutadapt.def
new file mode 100644
index 0000000000000000000000000000000000000000..90cafb605f282faf8fa836ef7eea5c6e99f8fa5d
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.14/cutadapt.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CUTADAPT_VERSION=1.14
+PACKAGES="bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             python3-pip \
+             gcc"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install setuptools
+pip3 install cutadapt==${CUTADAPT_VERSION}
+
+%environment
+export CUTADAPT_VERSION=1.14
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/cutadapt/1.15/build.sh b/src/singularity_modules/cutadapt/1.15/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c002354b7e4c92bf9a03e7fafe89214f74a98012
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.15/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/cutadapt:1.15.sif src/singularity_modules/cutadapt/1.15/cutadapt.def && \
+singularity sign bin/cutadapt:1.15.sif
diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt.def b/src/singularity_modules/cutadapt/1.15/cutadapt.def
new file mode 100644
index 0000000000000000000000000000000000000000..041f3a18dd8fea721bedb3e39cd9b0ab0f73187c
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.15/cutadapt.def
@@ -0,0 +1,28 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CUTADAPT_VERSION=1.15
+PACKAGES="bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             python3-pip \
+             gcc"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install setuptools
+pip3 install cutadapt==${CUTADAPT_VERSION}
+
+%environment
+export CUTADAPT_VERSION=1.14
+
+%runscript
+exec /bin/bash "$@"
+xec /bin/bash "$@"
diff --git a/src/singularity_modules/deeptools/3.0.2/build.sh b/src/singularity_modules/deeptools/3.0.2/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9e59a81d43cae27b5278dc5cc18a39016ab8c8e1
--- /dev/null
+++ b/src/singularity_modules/deeptools/3.0.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/deeptools:3.0.2.sif src/singularity_modules/deeptools/3.0.2/deeptools.def && \
+singularity sign bin/deeptools:3.0.2.sif
diff --git a/src/singularity_modules/deeptools/3.0.2/deeptools.def b/src/singularity_modules/deeptools/3.0.2/deeptools.def
new file mode 100644
index 0000000000000000000000000000000000000000..dc8fbdca863c92e777b3a09237f3439e69f6beba
--- /dev/null
+++ b/src/singularity_modules/deeptools/3.0.2/deeptools.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: debian:stretch
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+DEEPTOOLS_VERSION=3.0.2
+PACKAGES="build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             libcurl4-gnutls-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install deeptools==${DEEPTOOLS_VERSION}
+
+%environment
+export DEEPTOOLS_VERSION=3.0.2
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/deeptools/3.1.1/build.sh b/src/singularity_modules/deeptools/3.1.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..b9210571f8a0e2e0bdbb4fd837db41261ed4984e
--- /dev/null
+++ b/src/singularity_modules/deeptools/3.1.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/deeptools:3.1.1.sif src/singularity_modules/deeptools/3.1.1/deeptools.def && \
+singularity sign bin/deeptools:3.1.1.sif
diff --git a/src/singularity_modules/deeptools/3.1.1/deeptools.def b/src/singularity_modules/deeptools/3.1.1/deeptools.def
new file mode 100644
index 0000000000000000000000000000000000000000..366b6218020116097819a2d519e99c7c6c1904e9
--- /dev/null
+++ b/src/singularity_modules/deeptools/3.1.1/deeptools.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: debian:stretch
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+DEEPTOOLS_VERSION=3.1.1
+PACKAGES="build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             libcurl4-gnutls-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install deeptools==${DEEPTOOLS_VERSION}
+
+%environment
+export DEEPTOOLS_VERSION=3.0.2
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/docker_to_singularity.sh b/src/singularity_modules/docker_to_singularity.sh
new file mode 100644
index 0000000000000000000000000000000000000000..0a71bfbccb414bbd3b24bc98612321200ca8b4c8
--- /dev/null
+++ b/src/singularity_modules/docker_to_singularity.sh
@@ -0,0 +1,13 @@
+# install spython
+# sudo pip3 install spython
+
+find src/docker_modules/ -name "Dockerfile" | \
+  perl -pe "s/docker/singularity/g" | \
+  perl -pe "s/Dockerfile//g" | \
+  awk '{system("mkdir -p " $0)}'
+
+find src/docker_modules/ -name "Dockerfile" | \
+  perl -pe "s/(^.*$)/spython recipe \1 > \1/g" | \
+  perl -pe "s/(^.*)docker_modules(.*$)/\1singularity_modules\2/g" | \
+  perl -pe "s/(^.*\/([^\/]*)\/[^\/]*\/)Dockerfile$/\1\2.def/g" | \
+  awk '{system($0)}'
diff --git a/src/singularity_modules/fastp/0.19.7/build.sh b/src/singularity_modules/fastp/0.19.7/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..01a0d8121ac842dc84113b94aa6a6f7c1ca4c043
--- /dev/null
+++ b/src/singularity_modules/fastp/0.19.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/fastp:0.19.7.sif docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0 && \
+singularity sign bin/fastp:0.19.7.sif
diff --git a/src/singularity_modules/fastqc/0.11.5/build.sh b/src/singularity_modules/fastqc/0.11.5/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..b3983367f70e5b7aa19b699d81dd0198b2b9c4da
--- /dev/null
+++ b/src/singularity_modules/fastqc/0.11.5/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/fastqc:0.11.5.sif src/singularity_modules/fastqc/0.11.5/fastqc.def && \
+singularity sign bin/fastqc:0.11.5.sif
diff --git a/src/singularity_modules/fastqc/0.11.5/fastqc.def b/src/singularity_modules/fastqc/0.11.5/fastqc.def
new file mode 100644
index 0000000000000000000000000000000000000000..d2bc5389676cca32fceb8377fd6d44db6efc8b85
--- /dev/null
+++ b/src/singularity_modules/fastqc/0.11.5/fastqc.def
@@ -0,0 +1,21 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+FASTQC_VERSION=0.11.5
+PACKAGES="fastqc=${FASTQC_VERSION}* \
+perl=5.26*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export FASTQC_VERSION=0.11.5
+export PACKAGES=fastqc=${FASTQC_VERSION}*
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/file_handle/0.1.1/build.sh b/src/singularity_modules/file_handle/0.1.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..17122f2430e98679a97d1eaadfdacbc0a980a346
--- /dev/null
+++ b/src/singularity_modules/file_handle/0.1.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/file_handle:0.1.1.sif src/singularity_modules/file_handle/0.1.1/file_handle.def && \
+singularity sign bin/file_handle:0.1.1.sif
diff --git a/src/singularity_modules/file_handle/0.1.1/file_handle.def b/src/singularity_modules/file_handle/0.1.1/file_handle.def
new file mode 100644
index 0000000000000000000000000000000000000000..f80a9aee38b09cb025c173625e3c9c95d660a08d
--- /dev/null
+++ b/src/singularity_modules/file_handle/0.1.1/file_handle.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+
+FILE_HANDLE_VERSION=0.1.1
+PACKAGES="git \
+ca-certificates "
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/LBMC/file_handle.git && \
+cd file_handle && \
+git checkout tags/v${FILE_HANDLE_VERSION} && \
+cp src/file_handle.py /usr/bin/file_handle.py && \
+chmod +x /usr/bin/file_handle.py
+
+%environment
+export FILE_HANDLE_VERSION=0.1.1
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/gatk/4.0.8.1/build.sh b/src/singularity_modules/gatk/4.0.8.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5158959fe830919751ce2906eddea4c29e99444e
--- /dev/null
+++ b/src/singularity_modules/gatk/4.0.8.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/gatk:4.0.8.1.sif src/singularity_modules/gatk/4.0.8.1/gatk.def && \
+singularity sign bin/gatk:4.0.8.1.sif
diff --git a/src/singularity_modules/gatk/4.0.8.1/gatk.def b/src/singularity_modules/gatk/4.0.8.1/gatk.def
new file mode 100644
index 0000000000000000000000000000000000000000..b13ef7ff00eda69d703aefa85b7bd0ecfd606cfd
--- /dev/null
+++ b/src/singularity_modules/gatk/4.0.8.1/gatk.def
@@ -0,0 +1,16 @@
+Bootstrap: docker
+From: broadinstitute/gatk:4.0.8.1
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+
+GATK_VERSION=4.0.8.1
+cp gatk/gatk /usr/bin/
+
+%environment
+export GATK_VERSION=4.0.8.1
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/hisat2/2.0.0/build.sh b/src/singularity_modules/hisat2/2.0.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e2b18756a8540739fa815f1ff3e3b4960b3e803b
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.0.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/hisat2:2.0.0.sif src/singularity_modules/hisat2/2.0.0/hisat2.def && \
+singularity sign bin/hisat2:2.0.0.sif
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2.def b/src/singularity_modules/hisat2/2.0.0/hisat2.def
new file mode 100644
index 0000000000000000000000000000000000000000..a3941bf3f874f72d0a6600d327959987db34a866
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.0.0/hisat2.def
@@ -0,0 +1,32 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Nicolas Fontrodona
+
+%post
+HISAT2_VERSION=2.0.0
+PACKAGES="unzip \
+gcc \
+g++ \
+make \
+curl \
+ca-certificates"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
+unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
+cd hisat2-${HISAT2_VERSION}-beta && \
+make && \
+cp hisat2 /usr/bin && \
+cp hisat2-* /usr/bin && \
+rm -Rf hisat2-${HISAT2_VERSION}-beta
+
+%environment
+export HISAT2_VERSION=2.0.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/htseq/0.8.0/build.sh b/src/singularity_modules/htseq/0.8.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..73b14c96de04064668445e3c309eddd4df269d67
--- /dev/null
+++ b/src/singularity_modules/htseq/0.8.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/htseq:0.8.0.sif src/singularity_modules/htseq/0.8.0/htseq.def && \
+singularity sign bin/htseq:0.8.0.sif
diff --git a/src/singularity_modules/htseq/0.8.0/htseq.def b/src/singularity_modules/htseq/0.8.0/htseq.def
new file mode 100644
index 0000000000000000000000000000000000000000..d315b301755ed5393cc603ba2323b2f2617de156
--- /dev/null
+++ b/src/singularity_modules/htseq/0.8.0/htseq.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+HTSEQ_VERSION=0.8.0
+PACKAGES="build-essential \
+python3-pip \
+python3-setuptools \
+python3-dev \
+python3-wheel"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install numpy==1.14.3
+pip3 install pysam==0.15.0
+pip3 install HTSeq==${HTSEQ_VERSION}
+
+%environment
+export HTSEQ_VERSION=0.8.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/kallisto/0.43.1/build.sh b/src/singularity_modules/kallisto/0.43.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8ecfe6e4b7121c57a6c03d72f149a6eca29c7f37
--- /dev/null
+++ b/src/singularity_modules/kallisto/0.43.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/kallisto:0.43.1.sif src/singularity_modules/kallisto/0.43.1/kallisto.def && \
+singularity sign bin/kallisto:0.43.1.sif
diff --git a/src/singularity_modules/kallisto/0.43.1/kallisto.def b/src/singularity_modules/kallisto/0.43.1/kallisto.def
new file mode 100644
index 0000000000000000000000000000000000000000..3b9899a03311a1bce2a8b6c1e8f83e861db773c1
--- /dev/null
+++ b/src/singularity_modules/kallisto/0.43.1/kallisto.def
@@ -0,0 +1,25 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+KALLISTO_VERSION=0.43.1
+PACKAGES="curl \
+ca-certificates"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
+rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
+
+%environment
+export KALLISTO_VERSION=0.44.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/kallisto/0.44.0/build.sh b/src/singularity_modules/kallisto/0.44.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..10a6cc0815f13d40ecb5a7f7919df27ffabc7fb3
--- /dev/null
+++ b/src/singularity_modules/kallisto/0.44.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/kallisto:0.44.0.sif src/singularity_modules/kallisto/0.44.0/kallisto.def && \
+singularity sign bin/kallisto:0.44.0.sif
diff --git a/src/singularity_modules/kallisto/0.44.0/kallisto.def b/src/singularity_modules/kallisto/0.44.0/kallisto.def
new file mode 100644
index 0000000000000000000000000000000000000000..613218ac11e326beac41405800ae317c2565482c
--- /dev/null
+++ b/src/singularity_modules/kallisto/0.44.0/kallisto.def
@@ -0,0 +1,25 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+KALLISTO_VERSION=0.44.0
+PACKAGES="curl \
+ca-certificates"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
+rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
+
+%environment
+export KALLISTO_VERSION=0.44.0
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/macs2/2.1.2/build.sh b/src/singularity_modules/macs2/2.1.2/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1ca311007fed8ba5497328078d7891b69efc5277
--- /dev/null
+++ b/src/singularity_modules/macs2/2.1.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/macs2:2.1.2.sif docker://quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1 && \
+singularity sign bin/macs2:2.1.2.sif
diff --git a/src/singularity_modules/macs2/2.1.2/macs2.def b/src/singularity_modules/macs2/2.1.2/macs2.def
new file mode 100644
index 0000000000000000000000000000000000000000..0b56223a2882aa70ef771fff67790d4b8fbcd9b5
--- /dev/null
+++ b/src/singularity_modules/macs2/2.1.2/macs2.def
@@ -0,0 +1,28 @@
+Bootstrap: docker
+From: ubuntu:18.04
+%labels
+MAINTAINER Laurent Modolo
+%post
+
+MACS_VERSION=2.1.2
+PACKAGES="git \
+build-essential \
+python-pip \
+ca-certificates \
+python-setuptools \
+python-dev \
+python-numpy \
+python-wheel \
+zlib1g-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip install MACS2==${MACS_VERSION}
+
+%environment
+export MACS_VERSION=2.1.1.20160309
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/multiqc/1.0/build.sh b/src/singularity_modules/multiqc/1.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..36f629810e3a7af6b5fae1904fa9f2f15a8b8e19
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/multiqc:1.0.sif src/singularity_modules/multiqc/1.0/multiqc.def && \
+singularity sign bin/multiqc:1.0.sif
diff --git a/src/singularity_modules/multiqc/1.0/multiqc.def b/src/singularity_modules/multiqc/1.0/multiqc.def
new file mode 100644
index 0000000000000000000000000000000000000000..195def47e3f70a53a2192d682d10efd3195787ae
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.0/multiqc.def
@@ -0,0 +1,39 @@
+Bootstrap: docker
+From: debian:stretch
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+MULTIQC_VERSION=1.0
+PACKAGES="build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+locale-gen en_US.UTF-8
+LC_ALL=en_US.utf-8
+LANG=en_US.utf-8
+LC_ALL=C.UTF-8
+LANG=C.UTF-8
+
+pip3 install multiqc==${MULTIQC_VERSION}
+
+%environment
+export KALLISTO_VERSION=0.44.0
+export locale-gen en_US.UTF-8
+export LC_ALL=en_US.utf-8
+export LANG=en_US.utf-8
+export LC_ALL=C.UTF-8
+export LANG=C.UTF-8
+
+%runscript
+exec /bin/bash "$@"
+
diff --git a/src/singularity_modules/multiqc/1.7/build.sh b/src/singularity_modules/multiqc/1.7/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7c2ae6706849dff18a1fc20648d1146dbae74270
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/multiqc:1.7.sif src/singularity_modules/multiqc/1.7/multiqc.def && \
+singularity sign bin/multiqc:1.7.sif
diff --git a/src/singularity_modules/multiqc/1.7/multiqc.def b/src/singularity_modules/multiqc/1.7/multiqc.def
new file mode 100644
index 0000000000000000000000000000000000000000..db345390d4ff15e9bec55c7edc75df96eb8d122c
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.7/multiqc.def
@@ -0,0 +1,39 @@
+Bootstrap: docker
+From: debian:stretch
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+MULTIQC_VERSION=1.7
+PACKAGES="build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+locale-gen en_US.UTF-8
+LC_ALL=en_US.utf-8
+LANG=en_US.utf-8
+LC_ALL=C.UTF-8
+LANG=C.UTF-8
+
+pip3 install multiqc==${MULTIQC_VERSION}
+
+%environment
+export KALLISTO_VERSION=0.44.0
+export locale-gen en_US.UTF-8
+export LC_ALL=en_US.utf-8
+export LANG=en_US.utf-8
+export LC_ALL=C.UTF-8
+export LANG=C.UTF-8
+
+%runscript
+exec /bin/bash "$@"
+
diff --git a/src/singularity_modules/music/6613c53/build.sh b/src/singularity_modules/music/6613c53/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..94b5e31a1735262c32af79c281ddcccfb25702fb
--- /dev/null
+++ b/src/singularity_modules/music/6613c53/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/music:6613c53.sif src/singularity_modules/music/6613c53/music.def && \
+singularity sign bin/music:6613c53.sif
diff --git a/src/singularity_modules/music/6613c53/music.def b/src/singularity_modules/music/6613c53/music.def
new file mode 100644
index 0000000000000000000000000000000000000000..57a429047a561475ff170fdec4586fe4ccefbf57
--- /dev/null
+++ b/src/singularity_modules/music/6613c53/music.def
@@ -0,0 +1,50 @@
+Bootstrap: docker
+From: alpine:3.8
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+MUSIC_VERSION=6613c53
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+             make \
+             gcc \
+             g++ \
+             musl-dev \
+             zlib-dev \
+             ncurses-dev \
+             bzip2-dev \
+             xz-dev \
+             ca-certificates \
+             bash"
+
+apk update && \
+apk add ${PACKAGES}
+
+curl -L -o samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+    http://jaist.dl.sourceforge.net/project/samtools/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && tar jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2  \
+ && cd samtools-${SAMTOOLS_VERSION}/ \
+ && ./configure --without-curses \
+ && make \
+ && make install
+
+git clone https://github.com/gersteinlab/MUSIC.git && \
+cd MUSIC && \
+git checkout ${MUSIC_VERSION} && \
+make clean && \
+make  && \
+cd .. && \
+mv MUSIC/bin/MUSIC /usr/bin/ && \
+mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
+mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
+rm -Rf MUSIC
+
+chmod +x /usr/bin/*
+
+%environment
+export MUSIC_VERSION=6613c53
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/picard/2.18.11/PicardCommandLine b/src/singularity_modules/picard/2.18.11/PicardCommandLine
new file mode 100644
index 0000000000000000000000000000000000000000..ce067365785f2f03c722668eff8d80a94b9b34d3
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/PicardCommandLine
@@ -0,0 +1,15 @@
+#!/bin/sh
+set -eu
+PRG="$(basename -- "$0")"
+case "$PRG" in
+picard-tools)
+        echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
+        ;;
+PicardCommandLine)
+        ;;
+*)
+        set -- "$PRG" "$@"
+        ;;
+esac
+
+exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
diff --git a/src/singularity_modules/picard/2.18.11/build.sh b/src/singularity_modules/picard/2.18.11/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2c985f4e7ba9e7c1d74eef126c5597edde831235
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/picard:2.18.11.sif src/singularity_modules/picard/2.18.11/picard.def && \
+singularity sign bin/picard:2.18.11.sif
diff --git a/src/singularity_modules/picard/2.18.11/picard.def b/src/singularity_modules/picard/2.18.11/picard.def
new file mode 100644
index 0000000000000000000000000000000000000000..27a3e18aa7151ca50598ee7248b0ece63a25b6e7
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/picard.def
@@ -0,0 +1,30 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%files
+src/singularity_modules/picard/2.18.11/PicardCommandLine /usr/bin/
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+PICARD_VERSION=2.18.11
+PACKAGES="default-jre \
+curl \
+ca-certificates"
+
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
+mkdir -p /usr/share/java/  && \
+mv picard.jar /usr/share/java/
+chmod +x /usr/bin/PicardCommandLine
+
+%environment
+export PICARD_VERSION=2.18.11
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/pigz/2.4/build.sh b/src/singularity_modules/pigz/2.4/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9c1bfee094062d8c9b1d40965d7a6ac5924958c1
--- /dev/null
+++ b/src/singularity_modules/pigz/2.4/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/pigz:2.4.sif src/singularity_modules/pigz/2.4/pigz.def && \
+singularity sign bin/pigz:2.4.sif
diff --git a/src/singularity_modules/pigz/2.4/pigz.def b/src/singularity_modules/pigz/2.4/pigz.def
new file mode 100644
index 0000000000000000000000000000000000000000..63e2d24663f603ed88b90bb00b2d1aa3203649c5
--- /dev/null
+++ b/src/singularity_modules/pigz/2.4/pigz.def
@@ -0,0 +1,20 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+PIGZ_VERSION=2.4
+PACKAGES=pigz=${PIGZ_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export PIGZ_VERSION=2.4
+export PACKAGES=pigz=${PIGZ_VERSION}*
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/rsem/1.3.0/build.sh b/src/singularity_modules/rsem/1.3.0/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..de64794a33d098c07e4f959679af258e48eb462d
--- /dev/null
+++ b/src/singularity_modules/rsem/1.3.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/rsem:1.3.0.sif src/singularity_modules/rsem/1.3.0/rsem.def && \
+singularity sign bin/rsem:1.3.0.sif
diff --git a/src/singularity_modules/rsem/1.3.0/rsem.def b/src/singularity_modules/rsem/1.3.0/rsem.def
new file mode 100644
index 0000000000000000000000000000000000000000..2e615b0d051ef500b60f9673faa7fe410ff8059c
--- /dev/null
+++ b/src/singularity_modules/rsem/1.3.0/rsem.def
@@ -0,0 +1,36 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+RSEM_VERSION=1.3.0
+BOWTIE2_VERSION=2.3.4.1
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+build-essential \
+ca-certificates \
+zlib1g-dev \
+bowtie2=${BOWTIE2_VERSION}* \
+samtools=${SAMTOOLS_VERSION}*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/deweylab/RSEM.git RSEM_${RSEM_VERSION} && \
+cd RSEM_${RSEM_VERSION} && \
+git checkout tags/v${RSEM_VERSION} && \
+make && \
+cd .. && \
+mv RSEM_${RSEM_VERSION}/rsem-* RSEM_${RSEM_VERSION}/rsem_* RSEM_${RSEM_VERSION}/convert-* RSEM_${RSEM_VERSION}/extract-* /usr/bin/ && \
+rm -Rf RSEM_${RSEM_VERSION}
+
+%environment
+export RSEM_VERSION=1.3.0
+export BOWTIE2_VERSION=2.3.4.1
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/salmon/0.8.2/build.sh b/src/singularity_modules/salmon/0.8.2/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..42464c1c83e52c9260679edeef33ccc9faab07c8
--- /dev/null
+++ b/src/singularity_modules/salmon/0.8.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/salmon:0.8.2.sif src/singularity_modules/salmon/0.8.2/salmon.def && \
+singularity sign bin/salmon:0.8.2.sif
diff --git a/src/singularity_modules/salmon/0.8.2/salmon.def b/src/singularity_modules/salmon/0.8.2/salmon.def
new file mode 100644
index 0000000000000000000000000000000000000000..d23673a4d3ddc3a82d1d1519b29e560ef7dc9f60
--- /dev/null
+++ b/src/singularity_modules/salmon/0.8.2/salmon.def
@@ -0,0 +1,25 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SALMON_VERSION=0.8.2
+PACKAGES="curl \
+ca-certificates"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L  https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz -o Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
+tar xzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
+mv Salmon-${SALMON_VERSION}_linux_x86_64/bin/* /usr/bin/ && \
+rm -Rf Salmon-${SALMON_VERSION}*
+
+%environment
+export SALMON_VERSION=0.8.2
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/sambamba/0.6.7/build.sh b/src/singularity_modules/sambamba/0.6.7/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fad93ead5827ff2fe6aadd0504a43d11ede728e6
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def && \
+singularity sign bin/sambamba:0.6.7.sif
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba.def b/src/singularity_modules/sambamba/0.6.7/sambamba.def
new file mode 100644
index 0000000000000000000000000000000000000000..f94a1b8beb21d12e16629cd8954ee755c0354512
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.7/sambamba.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMBAMBA_VERSION=0.6.7
+PACKAGES="curl=7.58.0* \
+ca-certificates=20180409 \
+build-essential=12.4* \
+zlib1g-dev=1:1.2.11*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+
+%environment
+export SAMBAMBA_VERSION=0.6.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/samblaster/0.1.24/build.sh b/src/singularity_modules/samblaster/0.1.24/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9a5b9fecc61d3a78de5a0d18a4b73baa7c2004a1
--- /dev/null
+++ b/src/singularity_modules/samblaster/0.1.24/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/samblaster:0.1.24.sif src/singularity_modules/samblaster/0.1.24/samblaster.def && \
+singularity sign bin/samblaster:0.1.24.sif
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster.def b/src/singularity_modules/samblaster/0.1.24/samblaster.def
new file mode 100644
index 0000000000000000000000000000000000000000..d2abfd55e3474979ca7dca8e10bb231bbacb9964
--- /dev/null
+++ b/src/singularity_modules/samblaster/0.1.24/samblaster.def
@@ -0,0 +1,30 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMBLASTER_VERSION=0.1.24
+PACKAGES="curl \
+ca-certificates \
+build-essential \
+zlib1g-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
+
+%environment
+export SAMBLASTER_VERSION=0.1.24
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/samtools/1.7/build.sh b/src/singularity_modules/samtools/1.7/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5e720251c9994a202703928605b323f19d51387c
--- /dev/null
+++ b/src/singularity_modules/samtools/1.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/samtools:1.7.sif src/singularity_modules/samtools/1.7/samtools.def && \
+singularity sign bin/samtools:1.7.sif
diff --git a/src/singularity_modules/samtools/1.7/samtools.def b/src/singularity_modules/samtools/1.7/samtools.def
new file mode 100644
index 0000000000000000000000000000000000000000..c73f4e840ff3a9bd5c8be65e8fbbfab66c8b7910
--- /dev/null
+++ b/src/singularity_modules/samtools/1.7/samtools.def
@@ -0,0 +1,35 @@
+Bootstrap: docker
+From: alpine:3.8
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+             make \
+             gcc \
+             musl-dev \
+             zlib-dev \
+             ncurses-dev \
+             bzip2-dev \
+             xz-dev \
+             bash"
+apk update && \
+apk add ${PACKAGES}
+
+git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION}  && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
+
+%environment
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/sratoolkit/2.8.2/build.sh b/src/singularity_modules/sratoolkit/2.8.2/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fd8586e38a57fbb56262a081215ce95070c555e1
--- /dev/null
+++ b/src/singularity_modules/sratoolkit/2.8.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/sratoolkit:2.8.2.sif src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def && \
+singularity sign bin/sratoolkit:2.8.2.sif
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
new file mode 100644
index 0000000000000000000000000000000000000000..7fd70f27bbb10d8e78268431b143d422f9b6dc40
--- /dev/null
+++ b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SRATOOLKIT_VERSION=2.8.2
+PACKAGES=sra-toolkit=${SRATOOLKIT_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export SRATOOLKIT_VERSION=2.8.2
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/subread/1.6.4/build.sh b/src/singularity_modules/subread/1.6.4/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..029a7d84e5bd22e314eb2fa7d912b2771af66ac8
--- /dev/null
+++ b/src/singularity_modules/subread/1.6.4/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/subread:1.6.4.sif docker://quay.io/biocontainers/subread:1.6.4--h84994c4_1 && \
+singularity sign bin/subread:1.6.4.sif
diff --git a/src/singularity_modules/tophat/2.1.1/build.sh b/src/singularity_modules/tophat/2.1.1/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d0e2144537fd3f9a09180a92f6a2b74961e4f85b
--- /dev/null
+++ b/src/singularity_modules/tophat/2.1.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/tophat:2.1.1.sif src/singularity_modules/tophat/2.1.1/tophat.def && \
+singularity sign bin/tophat:2.1.1.sif
diff --git a/src/singularity_modules/tophat/2.1.1/tophat.def b/src/singularity_modules/tophat/2.1.1/tophat.def
new file mode 100644
index 0000000000000000000000000000000000000000..c683ba380f6dfbb105c0c57b6380e533568dda82
--- /dev/null
+++ b/src/singularity_modules/tophat/2.1.1/tophat.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+TOPHAT_VERSION=2.1.1
+PACKAGES=tophat=${BOWTIE2_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export TOPHAT_VERSION=2.1.1
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/trimmomatic/0.36/build.sh b/src/singularity_modules/trimmomatic/0.36/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3b3d8728817016dd928bca2a10c8b45743ad7d70
--- /dev/null
+++ b/src/singularity_modules/trimmomatic/0.36/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/trimmomatic:0.36.sif src/singularity_modules/trimmomatic/0.36/trimmomatic.def && \
+singularity sign bin/trimmomatic:0.36.sif
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/singularity_modules/trimmomatic/0.36/trimmomatic.def
new file mode 100644
index 0000000000000000000000000000000000000000..417e863d1a7b5dc5bddb28e7fa8d293d533c78dd
--- /dev/null
+++ b/src/singularity_modules/trimmomatic/0.36/trimmomatic.def
@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+TRIMMOMATIC_VERSION=0.36
+PACKAGES=trimmomatic=${TRIMMOMATIC_VERSION}*
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export TRIMMOMATIC_VERSION=0.36
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/ucsc/375/build.sh b/src/singularity_modules/ucsc/375/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ab60035f4e9f3bfa9b33a221c348c4b7de02538b
--- /dev/null
+++ b/src/singularity_modules/ucsc/375/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/ucsc:375.sif src/singularity_modules/ucsc/375/ucsc.def && \
+singularity sign bin/ucsc:375.sif
diff --git a/src/singularity_modules/ucsc/375/ucsc.def b/src/singularity_modules/ucsc/375/ucsc.def
new file mode 100644
index 0000000000000000000000000000000000000000..a1d1a743acebd586c141a8b6841e8e824856c8f6
--- /dev/null
+++ b/src/singularity_modules/ucsc/375/ucsc.def
@@ -0,0 +1,36 @@
+Bootstrap: docker
+From: debian:jessie
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+UCSC_VERSION=375
+PACKAGES="apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             rsync"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+cd .. &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps
+
+%environment
+export UCSC_VERSION=375
+
+%runscript
+exec /bin/bash "$@"
+
diff --git a/src/singularity_modules/umitools/0.3.4/build.sh b/src/singularity_modules/umitools/0.3.4/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8ccd233e4738b0599337e7c280d5f837fa6a06bf
--- /dev/null
+++ b/src/singularity_modules/umitools/0.3.4/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/umitools:0.3.4.sif docker://quay.io/biocontainers/umitools:0.3.4--py37_1 && \
+singularity sign bin/umitools:0.3.4.sif
diff --git a/src/singularity_modules/umitools/0.3.4/umitools.def b/src/singularity_modules/umitools/0.3.4/umitools.def
new file mode 100644
index 0000000000000000000000000000000000000000..4d1dd2affd9e8a9699916db07285bd4b43fd5b20
--- /dev/null
+++ b/src/singularity_modules/umitools/0.3.4/umitools.def
@@ -0,0 +1,28 @@
+Bootstrap: docker
+From: ubuntu:18.04
+%labels
+MAINTAINER Laurent Modolo
+%post
+
+UMITOOLS_VERSION=0.3.4
+PACKAGES="git \
+build-essential \
+python-pip \
+ca-certificates \
+python-setuptools \
+python-dev \
+python-numpy \
+python-wheel \
+zlib1g-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip install umitools==${UMITOOLS_VERSION}
+
+%environment
+export UMITOOLS_VERSION=0.3.4
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/singularity_modules/urqt/d62c1f8/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7ad1eb6c41f15b94e7fb8294e34984a53d6f9c19
--- /dev/null
+++ b/src/singularity_modules/urqt/d62c1f8/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/urqt:d62c1f8.sif src/singularity_modules/urqt/d62c1f8/urqt.def && \
+singularity sign bin/urqt:d62c1f8.sif
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt.def b/src/singularity_modules/urqt/d62c1f8/urqt.def
new file mode 100644
index 0000000000000000000000000000000000000000..6bfeb23f9c4a7d0f8bac94b92eb4d0ec62adb932
--- /dev/null
+++ b/src/singularity_modules/urqt/d62c1f8/urqt.def
@@ -0,0 +1,31 @@
+Bootstrap: library
+From: debian:9
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+URQT_VERSION=d62c1f8
+PACKAGES="git \
+g++ \
+make \
+ca-certificates \
+zlib1g-dev"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/l-modolo/UrQt.git && \
+cd UrQt && \
+git checkout ${URQT_VERSION} && \
+make && \
+cd .. && \
+mv UrQt/UrQt /usr/bin/ && \
+rm -Rf UrQt
+
+%environment
+export URQT_VERSION=d62c1f8
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 00a471c6c4a356b9fd843e7185b6c440ea37bfcb..baebb4cf2fcebc4001c04c5f53842a3b74ebbf27 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -3,91 +3,237 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $build_synthetic_bed {
+      withName: build_synthetic_bed {
         container = "bedtools:2.25.0"
+        cpus = 1
       }
-      $fasta_from_bed {
+      withName: fasta_from_bed {
         container = "bedtools:2.25.0"
+        cpus = 1
       }
-      $index_fasta {
+      withName: index_fasta {
         container = "bowtie2:2.3.4.1"
+        cpus = 4
       }
-      $mapping_fastq_paired {
+      withName: mapping_fastq_paired {
         container = "bowtie2:2.3.4.1"
+        cpus = 4
+      }
+      withName: bam_2_fastq_paired {
+        container = "samtools:1.7"
+        cpus = 4
       }
-      $bam_2_fastq_paired {
+      withName: filter_bam_paired {
         container = "samtools:1.7"
+        cpus = 4
       }
-      $sort_bam_paired {
+      withName: sort_bam_paired {
         container = "samtools:1.7"
+        cpus = 4
       }
-      $index_bam_paired {
+      withName: index_bam_paired {
         container = "samtools:1.7"
+        cpus = 4
       }
-      $mapping_fastq_single {
+      withName: mapping_fastq_single {
         container = "bowtie2:2.3.4.1"
+        cpus = 4
       }
-      $bam_2_fastq_single {
+      withName: bam_2_fastq_single {
         container = "samtools:1.7"
+        cpus = 4
       }
-      $sort_bam_single {
+      withName: filter_bam_single {
         container = "samtools:1.7"
+        cpus = 4
       }
-      $index_bam_single {
+      withName: sort_bam_single {
         container = "samtools:1.7"
+        cpus = 4
+      }
+      withName: index_bam_single {
+        container = "samtools:1.7"
+        cpus = 4
       }
     }
   }
-  sge {
-    process{
-      $build_synthetic_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
-        executor = "sge"
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: build_synthetic_bed {
+        container = "file://bin/bedtools:2.25.0.sif"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-      $fasta_from_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
-        executor = "sge"
+      }
+      withName: fasta_from_bed {
+        container = "file://bin/bedtools:2.25.0.sif"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
       }
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+      withName: index_fasta {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+      withName: mapping_fastq_single {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+      withName: mapping_fastq_paired {
+        container = "file://bin/bowtie2:2.3.4.1.sif"
+        cpus = 4
+      }
+      withName: bam_2_fastq_paired {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
+      }
+      withName: filter_bam_paired {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
+      }
+      withName: sort_bam_paired {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $mapping_fastq_paired {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+      withName: index_bam_paired {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $bam_2_fastq_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+      withName: bam_2_fastq_single {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $sort_bam_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+      withName: filter_bam_single {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $index_bam_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+      withName: sort_bam_single {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $mapping_fastq_single {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+      withName: index_bam_single {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
-      $bam_2_fastq_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+    }
+  }
+  psmn {
+    process{
+      withName: build_synthetic_bed {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bedtools/2.25.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
-      $sort_bam_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+      withName: fasta_from_bed {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bedtools/2.25.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
-      $index_bam_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "20GB"
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: mapping_fastq_paired {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: bam_2_fastq_paired {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: sort_bam_paired {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: index_bam_paired {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: mapping_fastq_single {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: bam_2_fastq_single {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: sort_bam_single {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: index_bam_single {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }
diff --git a/src/update_tools.sh b/src/update_tools.sh
new file mode 100755
index 0000000000000000000000000000000000000000..57af5db8b119176f94fe0ac4b28043b3cd94dd91
--- /dev/null
+++ b/src/update_tools.sh
@@ -0,0 +1,92 @@
+#/bin/sh
+
+# A POSIX variable
+OPTIND=1
+
+# Initialize our own variables:
+tool=""
+version=""
+
+while getopts "h?v:t:p:" opt; do
+  case "${opt}" in
+  h|\?)
+    echo "update_tools.sh -t toolname -v tool_version -p tool_previous_version"
+    exit 0
+    ;;
+  v)
+    version=${OPTARG}
+    ;;
+  p)
+    prev_version=${OPTARG}
+    ;;
+  t)
+    tool=${OPTARG}
+    ;;
+  esac
+done
+
+echo "tool=${tool}, version='${version}', previous version='${version}'"
+
+docker_tool_dir="src/docker_modules/"${tool}"/"
+echo ${docker_tool_dir}
+if [ -d ${docker_tool_dir} ]; then
+  echo "docker module found for ${tool}."
+  if [ -d ${docker_tool_dir}${version} ]; then
+    echo "version already existing, skipping."
+  else
+    cp -R ${docker_tool_dir}${prev_version} ${docker_tool_dir}${version}
+    sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/Dockerfile"
+    sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/docker_init.sh"
+    echo "docker_module for ${tool}:${version}, done."
+  fi
+else
+  echo "docker module not found for '${tool}', skipping."
+fi
+
+singularity_tool_dir="src/singularity_modules/"${tool}"/"
+echo ${singularity_tool_dir}
+if [ -d ${singularity_tool_dir} ]; then
+  echo "singularity module found for $tool."
+  if [ -d ${singularity_tool_dir}${version} ]; then
+    echo "version already existing, skipping."
+  else
+    cp -R ${singularity_tool_dir}${prev_version} ${singularity_tool_dir}${version}
+    sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/${tool}.def"
+    sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/build.sh"
+    echo "singularity_module for ${tool}:${version}, done."
+  fi
+else
+  echo "singularity module not found for '${tool}', skipping."
+fi
+
+nf_tool_dir="src/nf_modules/"$tool"/"
+echo $nf_tool_dir
+if [ -d ${nf_tool_dir} ]; then
+  echo "nf module found for ${tool}."
+  find ${nf_tool_dir} -maxdepth 1 -mindepth 1 -type f -name "*.config" |
+    awk "{system(\"sed -i \\\"s|${prev_version}|${version}|g\\\" \"\$0)}"
+  echo "nf_module for ${tool}:${version}, done."
+else
+  echo "nf module not found for '${tool}', skipping."
+fi
+
+psmn_modules_dir="src/psmn_modules/.git/"
+if [ ! -d ${nf_tool_dir} ]; then
+  git submodule init && \
+  git submodule update
+fi
+psmn_tool_app_dir="src/psmn_modules/apps/"${tool}"/"
+psmn_tool_module_dir="src/psmn_modules/modulefiles/"${tool}"/"
+echo ${psmn_tool_app_dir}
+if [ -d ${psmn_tool_app_dir} ]; then
+  echo "psmn module found for ${tool}."
+  cp ${psmn_tool_app_dir}/install_${prev_version}.sh \
+    ${psmn_tool_app_dir}/install_${version}.sh
+  sed -i "s|$prev_version|$version|g" ${psmn_tool_app_dir}/install_${version}.sh
+  cp ${psmn_tool_module_dir}/${prev_version}.lua \
+    ${psmn_tool_module_dir}/${version}.lua
+  sed -i "s|${prev_version}|${version}|g" ${psmn_tool_module_dir}/${version}.lua
+  echo "psmn_module for ${tool}:${version}, done."
+else
+  echo "psmn module not found for '${tool}', skipping."
+fi