diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md
index 695a16ec3855102584ce48b1c63787213bae99d9..1b15a64813a6505cd3623431ab701cd3807f3df3 100644
--- a/doc/TP_computational_biologists.md
+++ b/doc/TP_computational_biologists.md
@@ -180,3 +180,62 @@ After pushing your modifications on your forked repository, you can make a Merge
You can read more on this process [here](https://guides.github.com/introduction/flow/)
+
+### `docker_modules`
+
+The `src/docker_modules` contains the code to wrap tools in [Docker](https://www.docker.com/what-docker). [Docker](https://www.docker.com/what-docker) is a framework that allows you to execute software within [containers](https://www.docker.com/what-container). The `docker_modules` contains directory corresponding to tools and subdirectories corresponding to their version.
+
+```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/
+```
+
+To each `tools/version` corresponds two files:
+
+```sh
+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*
+```
+
+The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recipe to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in its `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
+
+By running this script you will be able to easily install tools in different versions on your personal computer and use it in your pipeline. Some of the advantages are:
+
+- Whatever the computer, the installation and the results will be the same
+- You can keep [container](https://www.docker.com/what-container) for old version of tools and run it on new systems (science = reproducibility)
+- 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.
+
+### `psmn_modules`
+
+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
+```
+
+Like the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recipes to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version.
+The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md) file of the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository contains all the instruction to be able to load the modules maintained by the LBMC and present in the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository.
+
+## Create your Docker containers
+
+For this practical, we are going to need the following tools:
+
+- For Illumina adaptor removal: cutadapt
+- For reads trimming by quality: UrQt
+- For mapping and quantifying reads: BEDtools and Kallisto
+
+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 commands:**
+
+```sh
+docker rm $(docker stop $(docker ps -aq))
+docker rmi $(docker images -qf "dangling=true")
+```
+
+
diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 1a2f3857c24702c4fa4430a97d51658f834fdea8..03e9928a386f2ff64a6ee8a753c523592c8f05b5 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -26,11 +26,11 @@ You are going to build a pipeline for you or your team. So the first step is to
## Forking
Instead of reinventing the wheel, you can use the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) as a template.
-To easily do so, go to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) repository and click on the [**fork**](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new) button.
+To easily do so, go to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) repository and click on the [**fork**](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new) button (you need to log-in).
-In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository (here [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow)) create a merge request. Merge requests are sent to the source repository to ask the maintainers to integrate modifications.
+In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository create a merge request (here [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow)). Merge requests are sent to the source repository to ask the maintainers to integrate modifications.
@@ -51,47 +51,7 @@ The [results](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master
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 `psmn_modules` folder.
-
-### `docker_modules`
-
-The `src/docker_modules` contains the code to wrap tools in [Docker](https://www.docker.com/what-docker). [Docker](https://www.docker.com/what-docker) is a framework that allows you to execute software within [containers](https://www.docker.com/what-container). The `docker_modules` contains directory corresponding to tools and subdirectories corresponding to their version.
-
-```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/
-```
-
-To each `tools/version` corresponds two files:
-
-```sh
-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*
-```
-
-The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recipe to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in its `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
-
-By running this script you will be able to easily install tools in different versions on your personal computer and use it in your pipeline. Some of the advantages are:
-
-- Whatever the computer, the installation and the results will be the same
-- You can keep [container](https://www.docker.com/what-container) for old version of tools and run it on new systems (science = reproducibility)
-- 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.
-
-### `psmn_modules`
-
-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
-```
-
-Like the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recipes to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version.
-The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md) file of the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository contains all the instruction to be able to load the modules maintained by the LBMC and present in the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository.
+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 one visible subdirectories `nf_modules` some pipeline examples and other hidden files.
### `nf_modules`
@@ -169,15 +129,12 @@ 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 https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
+git clone gitlab_lbmc:<usr_name>/nextflow.git
cd nextflow
src/install_nextflow.sh
```
@@ -186,7 +143,7 @@ We also need data to run our pipeline:
```
cd data
-git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+git clone gitlab_lbmc:LBMC/tiny_dataset.git
cd ..
```
@@ -249,23 +206,6 @@ You can run your pipeline again and check the content of the folder `results/sam
In this section you are going to build your own pipeline for RNASeq analysis from the code available in the `src/nf_modules` folder.
-## Create your Docker containers
-
-For this practical, we are going to need the following tools:
-
-- For Illumina adaptor removal: cutadapt
-- For reads trimming by quality: UrQt
-- For mapping and quantifying reads: BEDtools and Kallisto
-
-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 commands:**
-
-```sh
-docker rm $(docker stop $(docker ps -aq))
-docker rmi $(docker images -qf "dangling=true")
-```
-
## Cutadapt
The first step of the pipeline is to remove any Illumina adaptors left in your read files.
@@ -413,12 +353,13 @@ git config --global http.sslVerify false
git clone https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
cd nextflow/data
git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+git config --global http.sslVerify true
cd ..
```
## Run nextflow
-As we don’t want nextflow to be killed in case of disconnection, we start by launching `tmux`. In case of deconnection, you can restore your session with the command `tmux a`.
+As we don’t want nextflow to be killed in case of disconnection, we start by launching `tmux`. In case of deconnection, you can restore your session with the command `tmux a` and close one with `ctr + b + d`
```sh
tmux
diff --git a/doc/mail.txt b/doc/mail.txt
index e9f30cc646878f070cdc8b7dde4120120a0ae254..99a3f81d0fce926ce7524ce9b969d5249e6832c8 100644
--- a/doc/mail.txt
+++ b/doc/mail.txt
@@ -19,3 +19,24 @@ If you want to work on your laptop, or plan to work remotely on your desktop via
- docker
Best,
+
+Dear all,
+
+You registered to the formation Git (12/12) or/and the formation Nextlflow (13/12) from 13:30 pm to 18pm in the in the room M7.1H04.
+
+Please check that you have an account on our gitlab server at the following url :
+https://gitlab.biologie.ens-lyon.fr (only available from the ENS network)
+To connect, simply click on the CAS button.
+Your account is now linked to the gitlab server, but blocked
+You can send an email to laurent.modolo@ens-lyon.fr to activate your account.
+
+You will also need an account on the PSMN (http://www.ens-lyon.fr/PSMN/doku.php?id=contact:forms:inscription) (don’t wait until the 12 to request an account !)
+
+If you want to work on your laptop, or plan to work remotely on your desktop via ssh (http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/bioinfo_club/1_ssh_and_other_tools_to_work_remotly) you need to have the following software installed :
+- ssh
+- git
+- java (>=1.8) (for the nextflow formation)
+- docker (for the nextflow formation)
+Otherwise, you will need to request an account to use the computer in the room (http://www.cbp.ens-lyon.fr/doku.php?id=contact:compte)
+
+Best,
diff --git a/src/.conda_envs/gatk_4.0.8.1 b/src/.conda_envs/gatk_4.0.8.1
new file mode 120000
index 0000000000000000000000000000000000000000..96fb8371cfcc3d758cfcf4fe77e3c355b8579841
--- /dev/null
+++ b/src/.conda_envs/gatk_4.0.8.1
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/gatk_4.0.8.1
\ No newline at end of file
diff --git a/src/.conda_envs/ncdu b/src/.conda_envs/ncdu
new file mode 120000
index 0000000000000000000000000000000000000000..f46dbc261cbd16dd4221e4533b203dbdeeb46293
--- /dev/null
+++ b/src/.conda_envs/ncdu
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/ncdu
\ No newline at end of file
diff --git a/src/.conda_envs/python_mars_seq_modules b/src/.conda_envs/python_mars_seq_modules
new file mode 120000
index 0000000000000000000000000000000000000000..cd3910ea6920943ac21858b312917b05220ea5d7
--- /dev/null
+++ b/src/.conda_envs/python_mars_seq_modules
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/python_mars_seq_modules
\ No newline at end of file
diff --git a/src/.conda_envs/r_mars_seq_modules_r b/src/.conda_envs/r_mars_seq_modules_r
new file mode 120000
index 0000000000000000000000000000000000000000..00ebf61d64ebc9cfad5066797f23d1f460ff7be4
--- /dev/null
+++ b/src/.conda_envs/r_mars_seq_modules_r
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/r_mars_seq_modules_r
\ No newline at end of file
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
index bbf88057d7bff8c04a22c339d78f85fa24c6e4f8..909ca4cb6552d1b1da98dde03b210c5fa37bdd98 100644
--- a/src/.conda_packages.sh
+++ b/src/.conda_packages.sh
@@ -75,8 +75,11 @@ fi
if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
conda create --yes --name fastp_0.19.7 fastp=0.19.7
fi
-if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
- conda create --yes --name gatk_3.8 gatk=3.8
+if [ ! -d ${CONDA_ENVS}gatk_3.8.0 ]; then
+ conda create --yes --name gatk_3.8.0 gatk=3.8
+fi
+if [ ! -d ${CONDA_ENVS}gatk_4.0.8.1 ]; then
+ conda create --yes --name gatk_4.0.8.1 gatk4=4.0.8.1-0
fi
if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
conda create --yes --name cutadapt_1.14 cutadapt=1.14
diff --git a/src/.docker_modules/gatk/3.8.0/Dockerfile b/src/.docker_modules/gatk/3.8.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..185b9121939870446238396a3b7a1fbc30f7b8cc
--- /dev/null
+++ b/src/.docker_modules/gatk/3.8.0/Dockerfile
@@ -0,0 +1,4 @@
+FROM broadinstitute/gatk3:3.8-0
+MAINTAINER Laurent Modolo
+
+ENV GATK_VERSION=3.8.0
diff --git a/src/.docker_modules/gatk/3.8.0/docker_init.sh b/src/.docker_modules/gatk/3.8.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1188be23f86622450582486167064c6829913394
--- /dev/null
+++ b/src/.docker_modules/gatk/3.8.0/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/gatk:3.8.0
+docker build src/.docker_modules/gatk/3.8.0 -t 'lbmc/gatk:3.8.0'
+docker push lbmc/gatk:3.8.0
diff --git a/src/.docker_modules/htseq/0.11.2/Dockerfile b/src/.docker_modules/htseq/0.11.2/Dockerfile
index d9db9b1531282ad6bf91057c76a686c9cc707610..821d7760af2350605617aea694a92ff2470a9cb7 100644
--- a/src/.docker_modules/htseq/0.11.2/Dockerfile
+++ b/src/.docker_modules/htseq/0.11.2/Dockerfile
@@ -1,13 +1,12 @@
-
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV HTSEQ_VERSION=0.11.2
-ENV PACKAGES build-essential \
- python3-pip \
- python3-setuptools \
- python3-dev \
- python3-wheel
+ENV PACKAGES build-essential=12.4* \
+ python3-pip=9.0.1* \
+ python3-setuptools=39.0.1* \
+ python3-dev=3.6.7* \
+ python3-wheel=0.30.0*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
diff --git a/src/.docker_modules/htseq/0.11.2/docker_init.sh b/src/.docker_modules/htseq/0.11.2/docker_init.sh
old mode 100755
new mode 100644
index 9bd50893380dc1fb19736559551389934802eade..b46f01de71ede2fa99923f609cc98d96994a6bf6
--- a/src/.docker_modules/htseq/0.11.2/docker_init.sh
+++ b/src/.docker_modules/htseq/0.11.2/docker_init.sh
@@ -1,4 +1,2 @@
#!/bin/sh
-docker pull lbmc/htseq:0.11.2
-docker build src/.docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
-docker push lbmc/htseq:0.11.2
+docker build src/docker_modules/HTSeq/0.11.2 -t 'htseq:0.11.2'
diff --git a/src/.docker_modules/umi_tools/1.0.0/Dockerfile b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
index fee8aa46f3f27d30c0ea1bdcaee1a2abe974ac6e..d82cc9a6c7dc0877522149912b09899f7879ede9 100644
--- a/src/.docker_modules/umi_tools/1.0.0/Dockerfile
+++ b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
@@ -3,11 +3,18 @@ MAINTAINER Rémi SERAPHIN
ENV UMI_TOOLS_VERSION=1.0.0
ENV PACKAGES="bash \
- python3 \
- python3-dev \
- python3-pip \
- procps \
- gcc"
+ python3 \
+ python3-dev \
+ python3-pip \
+ procps \
+ zlib1g-dev \
+ zlib1g \
+ bzip2 \
+ libbz2-dev \
+ liblzma-dev \
+ libcurl4-openssl-dev \
+ make \t
+ gcc"
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 93e49c41c53cfa0b01ca92b67a2646cd19597cff..7a3302d7d6068d7e2bd71481064b99a91dc9da4f 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -23,7 +23,7 @@ profiles {
process{
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/${CONDA_ENVS}bedtools_2.25.0"
+ conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 13dfac50e21eb2b7a6bfbbd2cbad8bbceb6655cc..ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -23,7 +23,7 @@ profiles {
process{
withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -39,7 +39,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 13dfac50e21eb2b7a6bfbbd2cbad8bbceb6655cc..ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -23,7 +23,7 @@ profiles {
process{
withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -39,7 +39,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 222663bc4cf84889c3ee183930271cd4687f0ab2..8c158c0e72a5927b67cf1a4c106f7e22555e1cba 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -23,7 +23,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -39,7 +39,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 222663bc4cf84889c3ee183930271cd4687f0ab2..8c158c0e72a5927b67cf1a4c106f7e22555e1cba 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
cpus = 1
}
}
@@ -23,7 +23,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -39,7 +39,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "lbmc/cutadapt:2.1"
+ container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 5dfd26a2e2125034582ab419119092be396502bb..3ca188a0d614661f971529630df0870617b39f92 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withNamek index_fasta {
+ withName index_fasta {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}