diff --git a/README.md b/README.md
index c83d221d82c3d7995e040df35dc95dfacd5f6796..99142730308831f3fdc8772b482798833882df6d 100644
--- a/README.md
+++ b/README.md
@@ -73,7 +73,7 @@ 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
diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md
index 84138b44f821e7b6fb0d15dab0d385dc70b5f4ae..695a16ec3855102584ce48b1c63787213bae99d9 100644
--- a/doc/TP_computational_biologists.md
+++ b/doc/TP_computational_biologists.md
@@ -21,10 +21,10 @@ 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/
+$ 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 ../
@@ -32,15 +32,15 @@ drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../
 -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
@@ -80,8 +80,8 @@ 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 551 Jun 18 17:14 index.nf
 -rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf
@@ -89,12 +89,12 @@ total 12
 -rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
 ```
 
-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 [`.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 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).
+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`](./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 `psmn` and `docker` profile.
 
@@ -160,9 +160,9 @@ process{
 
 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 f0aac22ec3b4e6ad418b92af0093cfff907c3bfb..1a2f3857c24702c4fa4430a97d51658f834fdea8 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -59,16 +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*
 ```
@@ -322,7 +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/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.
+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.
 
@@ -340,7 +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/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.
+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.
 
@@ -348,7 +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/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).
+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:
 
@@ -360,7 +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 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).
+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.
 
diff --git a/src/docker_modules/bedtools/2.25.0/docker_init.sh b/src/docker_modules/bedtools/2.25.0/docker_init.sh
index c5c6f802290d6b629a949de8962709e3c5d7f258..63da76f2df7e2210f8e97c57b32f5c4ae010e394 100755
--- a/src/docker_modules/bedtools/2.25.0/docker_init.sh
+++ b/src/docker_modules/bedtools/2.25.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'
+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
index 8e010a67b74c0e5519d639c3cb06a14c1fb6f987..c8106dbf08e45df38e05b3dda6fb0e20dcec238b 100755
--- a/src/docker_modules/bowtie/1.2.2/docker_init.sh
+++ b/src/docker_modules/bowtie/1.2.2/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Bowtie/1.2.2 -t 'bowtie:1.2.2'
+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
index bba04c2bded6ebb0ba035ebead94b45effc7f486..77141d11131d21f7705aba955c271a2171a077d7 100755
--- a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
+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/docker_init.sh b/src/docker_modules/bwa/0.7.17/docker_init.sh
index 888bec687cbd7e16eb8908d3ef1d402bfaf9dc6e..d20312207e76e0dfd076e4130209dff1bbdd677e 100755
--- a/src/docker_modules/bwa/0.7.17/docker_init.sh
+++ b/src/docker_modules/bwa/0.7.17/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/BWA/0.7.17 -t 'bwa:0.7.17'
+docker build src/docker_modules/bwa/0.7.17 -t 'bwa:0.7.17'
diff --git a/src/docker_modules/deeptools/3.0.2/docker_init.sh b/src/docker_modules/deeptools/3.0.2/docker_init.sh
index ed0f069b1a759e5e13566add9212c853ca27df49..a2f152d2de03155d2055db8f8bdeb0c8585e135c 100755
--- a/src/docker_modules/deeptools/3.0.2/docker_init.sh
+++ b/src/docker_modules/deeptools/3.0.2/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/deepTools/3.0.2 -t 'deeptools:3.0.2'
+docker build src/docker_modules/deeptools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/docker_init.sh b/src/docker_modules/deeptools/3.1.1/docker_init.sh
index fb13a0a1824818cef1c764ce3e9a9a8251690acb..3c6782f0dd688006bafd2d59d3a2ff52a3f03a32 100755
--- a/src/docker_modules/deeptools/3.1.1/docker_init.sh
+++ b/src/docker_modules/deeptools/3.1.1/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/deepTools/3.1.1 -t 'deeptools:3.1.1'
+docker build src/docker_modules/deeptools/3.1.1 -t 'deeptools:3.1.1'
diff --git a/src/docker_modules/fastqc/0.11.5/docker_init.sh b/src/docker_modules/fastqc/0.11.5/docker_init.sh
index d8d557f5a93c4d163686285b8d5c0123006b3750..0c02fb709b3e9993124e08d88aec5700a0e32afb 100755
--- a/src/docker_modules/fastqc/0.11.5/docker_init.sh
+++ b/src/docker_modules/fastqc/0.11.5/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'
+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/docker_init.sh b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
index 34c497758976492553c1f5cb173203622382db06..31315f92ab7c76d59dc81f9eaf3c2ebb827ca38a 100755
--- a/src/docker_modules/gatk/4.0.8.1/docker_init.sh
+++ b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/GATK/4.0.8.1 -t 'gatk:4.0.8.1'
+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/docker_init.sh b/src/docker_modules/hisat2/2.0.0/docker_init.sh
index f497a67af04b382913f516d2b0fa78c4a00a0d26..428e28c464f38210862cf09e8f370d5bfbcb8357 100755
--- a/src/docker_modules/hisat2/2.0.0/docker_init.sh
+++ b/src/docker_modules/hisat2/2.0.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/HISAT2/2.0.0 -t 'hisat2:2.0.0'
+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
index 5b8415e2d4adeb65314a29d7cf7d386eba96e6cc..be46648e419daabc1e382da0885fafddd129f73c 100755
--- a/src/docker_modules/htseq/0.8.0/docker_init.sh
+++ b/src/docker_modules/htseq/0.8.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'
+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
index 8904daee8e494a755d44ab85f935c209ef80e5e1..08241603199a137dd3b6bcf52d53b239c237145a 100755
--- a/src/docker_modules/kallisto/0.43.1/docker_init.sh
+++ b/src/docker_modules/kallisto/0.43.1/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'
+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
index a17b82f5761976daacd7b909998af2f600264136..9e9e8c91350215ab62b815d3277fb75bcda9a6b5 100755
--- a/src/docker_modules/kallisto/0.44.0/docker_init.sh
+++ b/src/docker_modules/kallisto/0.44.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Kallisto/0.44.0 -t 'kallisto:0.44.0'
+docker build src/docker_modules/kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.0/docker_init.sh b/src/docker_modules/macs2/2.1.0/docker_init.sh
index 8af6fd7fe7139608a894fc053f987e6ef4b3380a..6c56575f79f1f43c17849f97f6c3eecde99d8bc5 100755
--- a/src/docker_modules/macs2/2.1.0/docker_init.sh
+++ b/src/docker_modules/macs2/2.1.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/MACS2/2.1.0 -t 'macs2:2.1.0'
+docker build src/docker_modules/macs2/2.1.0 -t 'macs2:2.1.0'
diff --git a/src/docker_modules/multiqc/1.0/docker_init.sh b/src/docker_modules/multiqc/1.0/docker_init.sh
index 7fb1b64ef11994fa6d555bf125242399dd7fce18..4c6de82afe5a0ce476399875ed701966da319f27 100755
--- a/src/docker_modules/multiqc/1.0/docker_init.sh
+++ b/src/docker_modules/multiqc/1.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/MultiQC/1.0 -t 'multiqc:1.0'
+docker build src/docker_modules/multiqc/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/music/6613c53/docker_init.sh b/src/docker_modules/music/6613c53/docker_init.sh
index c6163d6b58877cd3a7fd31be65fa2b9ee958c3d5..5daa39f1013e09253b8c52e1e481c4462e45cf26 100755
--- a/src/docker_modules/music/6613c53/docker_init.sh
+++ b/src/docker_modules/music/6613c53/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/MUSIC/6613c53 -t 'music:6613c53'
+docker build src/docker_modules/music/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/rsem/1.3.0/docker_init.sh b/src/docker_modules/rsem/1.3.0/docker_init.sh
index 5d788282b75adba0b372667e3a458a90b6aa4bfe..02d4bf9cc127f2a4ccc8592efd7c2aa79b28461b 100755
--- a/src/docker_modules/rsem/1.3.0/docker_init.sh
+++ b/src/docker_modules/rsem/1.3.0/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/RSEM/1.3.0 -t 'rsem:1.3.0'
+docker build src/docker_modules/rsem/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/docker_init.sh b/src/docker_modules/salmon/0.8.2/docker_init.sh
index ea75cf11004089375ff2dc56b619b08cb51955b2..5abdc6b06e792e0eb5c89248e8a240844bdd8a1a 100755
--- a/src/docker_modules/salmon/0.8.2/docker_init.sh
+++ b/src/docker_modules/salmon/0.8.2/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Salmon/0.8.2 -t 'salmon:0.8.2'
+docker build src/docker_modules/salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/samtools/1.7/docker_init.sh b/src/docker_modules/samtools/1.7/docker_init.sh
index 31916f45aa54dac20237de987b065153cd6022d9..03dc62e9a1d56d102a2ed5e4d251509dde689edb 100755
--- a/src/docker_modules/samtools/1.7/docker_init.sh
+++ b/src/docker_modules/samtools/1.7/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/SAMtools/1.7 -t 'samtools:1.7'
+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
index 501f769edecaf06b7a967d8b3aaecfb8e0ff7454..234100e8297fe288a64956074223a2185ff24bf9 100755
--- a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'
+docker build src/docker_modules/sratoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/tophat/2.1.1/docker_init.sh b/src/docker_modules/tophat/2.1.1/docker_init.sh
index 55e782f2fa5f6e45216c50fc86bc360fb8fa61b2..4dd0937a271053c5c3b56dfb0616107c8e0188b2 100755
--- a/src/docker_modules/tophat/2.1.1/docker_init.sh
+++ b/src/docker_modules/tophat/2.1.1/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/TopHat/2.1.1 -t 'tophat:2.1.1'
+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
index dd5c050d1c12a0a60b836e395a88f5a1a1f6e061..63bcdabfbaa8984022afc93ef92fbf014f9ad28c 100755
--- a/src/docker_modules/trimmomatic/0.36/docker_init.sh
+++ b/src/docker_modules/trimmomatic/0.36/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/Trimmomatic/0.36 -t 'trimmomatic:0.36'
+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
index 225589e021b151416048a8cf13f47bd3daa257d4..4c6c52692154697df95cdbbae2dfb5f184eae35b 100755
--- a/src/docker_modules/urqt/d62c1f8/docker_init.sh
+++ b/src/docker_modules/urqt/d62c1f8/docker_init.sh
@@ -1,2 +1,2 @@
 #!/bin/sh
-docker build src/docker_modules/UrQt/d62c1f8 -t 'urqt:d62c1f8'
+docker build src/docker_modules/urqt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/nf_modules/bedtools/tests.sh b/src/nf_modules/bedtools/tests.sh
index d493cdeaf83f5b9fc7631a7d4c501c99f5f4c0a5..61b3cc9c44bad7f171e87f180f2a2a156009d48f 100755
--- a/src/nf_modules/bedtools/tests.sh
+++ b/src/nf_modules/bedtools/tests.sh
@@ -1,13 +1,13 @@
-./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
-  -c src/nf_modules/BEDtools/fasta_from_bed.config \
+./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 \
+./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" \
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
index 3df87dfeb5230a2114ad1a9b7709433f20966ed2..65dfe80ed6e59614331cf99920f209dd3549709c 100755
--- a/src/nf_modules/bowtie/tests.sh
+++ b/src/nf_modules/bowtie/tests.sh
@@ -1,34 +1,34 @@
-./nextflow src/nf_modules/Bowtie/indexing.nf \
-  -c src/nf_modules/Bowtie/indexing.config \
+./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 \
+./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 \
+./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"
 
 if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/Bowtie/indexing.nf \
-  -c src/nf_modules/Bowtie/indexing.config \
+./nextflow src/nf_modules/bowtie/indexing.nf \
+  -c src/nf_modules/bowtie/indexing.config \
   -profile singularity \
   --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
 
-./nextflow src/nf_modules/Bowtie/mapping_single.nf \
-  -c src/nf_modules/Bowtie/mapping_single.config \
+./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"
 
-./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
-  -c src/nf_modules/Bowtie/mapping_paired.config \
+./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"
diff --git a/src/nf_modules/bowtie2/tests.sh b/src/nf_modules/bowtie2/tests.sh
index 01e349a7ccb3cce9c6afc9244e90abd9bb200656..bfec0d533a6430fb6cac928fe7350f3fa97a01ae 100755
--- a/src/nf_modules/bowtie2/tests.sh
+++ b/src/nf_modules/bowtie2/tests.sh
@@ -1,39 +1,39 @@
-./nextflow src/nf_modules/Bowtie2/indexing.nf \
-  -c src/nf_modules/Bowtie2/indexing.config \
+./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 \
+./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 \
+./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 \
+./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 \
+./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 \
+./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" \
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
index 8f3c52daf10f6c4c95da2d24e502b2118b17cd8b..2125e6c3ca5693324483f801c7630d8df406e252 100755
--- a/src/nf_modules/bwa/tests.sh
+++ b/src/nf_modules/bwa/tests.sh
@@ -1,17 +1,17 @@
-./nextflow src/nf_modules/BWA/indexing.nf \
-  -c src/nf_modules/BWA/indexing.config \
+./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 \
+# ./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 \
+./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" \
@@ -19,21 +19,21 @@
 
 
 if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/BWA/indexing.nf \
-  -c src/nf_modules/BWA/indexing.config \
+./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 \
+# ./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 \
+./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" \
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
index f6950b96a5d5ed56ed1fac24e1fbd9125d0cf7df..9100afcc042d2c0a0edd2075f527b071cdcc13cf 100755
--- a/src/nf_modules/deeptools/tests.sh
+++ b/src/nf_modules/deeptools/tests.sh
@@ -2,8 +2,8 @@
 
 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"
+./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"
 
-./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"
+./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"
 
-./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"
+./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"
diff --git a/src/nf_modules/fastqc/tests.sh b/src/nf_modules/fastqc/tests.sh
index de58b1028e221f05b7d084a7df6df5e8a077c4ec..1882ded7cfcd2f13dc2c9fa0a2d58d4f42e314af 100755
--- a/src/nf_modules/fastqc/tests.sh
+++ b/src/nf_modules/fastqc/tests.sh
@@ -1,9 +1,9 @@
-./nextflow src/nf_modules/FastQC/fastqc_paired.nf \
-  -c src/nf_modules/FastQC/fastqc_paired.config \
+./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 \
+./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/tests.sh b/src/nf_modules/htseq/tests.sh
index 4a2b5ceb62651dc0178fd026f29cd4310ecab29b..63e4ad516e671bdefa595878b31bc3eef67104d1 100755
--- a/src/nf_modules/htseq/tests.sh
+++ b/src/nf_modules/htseq/tests.sh
@@ -1,5 +1,5 @@
-./nextflow src/nf_modules/HTSeq/htseq.nf \
-  -c src/nf_modules/HTSeq/htseq.config \
+./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/tests.sh b/src/nf_modules/kallisto/tests.sh
index 0f69fcc40a2cc72aba93094560b2a239d2d42a76..cd87cf004ef314b7603444d808edb6e230e3810b 100755
--- a/src/nf_modules/kallisto/tests.sh
+++ b/src/nf_modules/kallisto/tests.sh
@@ -1,16 +1,16 @@
-./nextflow src/nf_modules/Kallisto/indexing.nf \
-  -c src/nf_modules/Kallisto/indexing.config \
+./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 \
+./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 \
+./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/multiqc/tests.sh b/src/nf_modules/multiqc/tests.sh
index 0e38a8e9e9710ec9e0d43a15432c8c8e96c0dfe0..baa1afaa7e3cf7c2aeaa667fbf12273194d07250 100755
--- a/src/nf_modules/multiqc/tests.sh
+++ b/src/nf_modules/multiqc/tests.sh
@@ -1,9 +1,9 @@
-./nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
-  -c src/nf_modules/MultiQC/multiqc_paired.config \
+./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 \
+./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/music/tests.sh b/src/nf_modules/music/tests.sh
index 7c6ad078ad2c27cbb378f8cdd6c505be9527fdef..23a62b4fc55fbcdd39afdda007aeaa760c45e6b4 100755
--- a/src/nf_modules/music/tests.sh
+++ b/src/nf_modules/music/tests.sh
@@ -1,6 +1,6 @@
 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 \
+./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" \
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
index 7d56b790607b7cc1128262f6439cb2b4d3d012ef..bfdba62aa0905b2d76c4c8a5534dfdf17cd9130e 100755
--- a/src/nf_modules/rsem/tests.sh
+++ b/src/nf_modules/rsem/tests.sh
@@ -1,17 +1,17 @@
-./nextflow src/nf_modules/RSEM/indexing.nf \
-  -c src/nf_modules/RSEM/indexing.config \
+./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 \
+./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 \
+./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/tests.sh b/src/nf_modules/samtools/tests.sh
index 9b7ac5e47388ea99ecf137ddd6add0b2ad313149..96a55e51f7ab109837fea9094965ff0c5beaa18c 100755
--- a/src/nf_modules/samtools/tests.sh
+++ b/src/nf_modules/samtools/tests.sh
@@ -1,20 +1,20 @@
-./nextflow src/nf_modules/SAMtools/sort_bams.nf \
-  -c src/nf_modules/SAMtools/sort_bams.config \
+./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 \
+./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 \
+./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 \
+./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/tests.sh b/src/nf_modules/sratoolkit/tests.sh
index d8575eb43181382f580699f5afd73f0ed69b9a2c..0321590e3d122a8e635d2e826b6864f6dbb0233f 100755
--- a/src/nf_modules/sratoolkit/tests.sh
+++ b/src/nf_modules/sratoolkit/tests.sh
@@ -1,4 +1,4 @@
-./nextflow src/nf_modules/SRAtoolkit/fastqdump.nf \
-  -c src/nf_modules/SRAtoolkit/fastqdump.config \
+./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"
+  --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
index cc8e32f4a5bf528dab305cc33e7524715ae9ca38..9992c67490ce65df42471a73d5c36bb0b708763e 100755
--- a/src/nf_modules/urqt/tests.sh
+++ b/src/nf_modules/urqt/tests.sh
@@ -1,24 +1,24 @@
-./nextflow src/nf_modules/UrQt/trimming_paired.nf \
-  -c src/nf_modules/UrQt/trimming_paired.config \
+./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 \
+./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 \
+./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 \
+./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
diff --git a/src/singularity_modules/UrQt/d62c1f8/build.sh b/src/singularity_modules/UrQt/d62c1f8/build.sh
deleted file mode 100755
index e003afadec5d6f75d9fb8e508c743875c7af4cff..0000000000000000000000000000000000000000
--- a/src/singularity_modules/UrQt/d62c1f8/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/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/bedtools/2.25.0/build.sh b/src/singularity_modules/bedtools/2.25.0/build.sh
index f72bd65650d353e9994fa652cd917da032ac51f6..91a1cfe3521e0650397663786a5c08c7a48be296 100755
--- a/src/singularity_modules/bedtools/2.25.0/build.sh
+++ b/src/singularity_modules/bedtools/2.25.0/build.sh
@@ -1,3 +1,3 @@
 #/bin/sh
-sudo singularity build --force bin/bedtools:2.25.0.sif src/singularity_modules/BEDtools/2.25.0/BEDtools.def
+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/bowtie/1.2.2/build.sh b/src/singularity_modules/bowtie/1.2.2/build.sh
index 2c7a0e6c8b1341d03d789db07363f10a4d08c530..29590dd35f57d2564a93ebd299d2ba4b7b8ab73a 100755
--- a/src/singularity_modules/bowtie/1.2.2/build.sh
+++ b/src/singularity_modules/bowtie/1.2.2/build.sh
@@ -1,3 +1,3 @@
 #/bin/sh
-sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/Bowtie/1.2.2/Bowtie.def
+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/build.sh b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
index 398fb1c79a1bb8b34d7dd1327824021906357abe..8d7c7f269f6ba4d762471025873ae7677e42aae2 100755
--- a/src/singularity_modules/bowtie2/2.3.4.1/build.sh
+++ b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
@@ -1,3 +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
+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
index 26b75effd1481f35a21642e90e7e0f99a11d09fd..91217c0d3970e97019af84f6ee1faccfcaa27cfa 100755
--- a/src/singularity_modules/bwa/0.7.17/build.sh
+++ b/src/singularity_modules/bwa/0.7.17/build.sh
@@ -1,3 +1,3 @@
 #/bin/sh
-sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/BWA/0.7.17/BWA.def
+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/UrQt/d62c1f8/UrQt.def b/src/singularity_modules/urqt/d62c1f8/UrQt.def
similarity index 100%
rename from src/singularity_modules/UrQt/d62c1f8/UrQt.def
rename to src/singularity_modules/urqt/d62c1f8/UrQt.def
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/singularity_modules/urqt/d62c1f8/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..81351fcc13f7b0570ecfef5b85442622cd608b2f
--- /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