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/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 4c8e39f2cf4ab1b2a7d30b7c04d18df75eb7dd8c..b1954161846133e0efe731c5a2245994a8e77e79 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -51,7 +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 `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`
@@ -82,9 +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
@@ -95,7 +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` files, there is 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
@@ -293,7 +293,7 @@ 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/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.
@@ -411,7 +411,7 @@ 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" -w /scratch/<login>
+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 :
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
index f4b744b71baea3607df8ea0b447e283c921f3455..6e198953a47de87a3535a78d515070adc7421467 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ b/src/nf_modules/BEDtools/fasta_from_bed.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BEDtools/2.25.0"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 607bda58f1061ef449df15d8eef17aa98a2b992d..4f9e69761261ed460aecbb3a96aac1bdba98951e 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$index_fasta {
beforeScript = "module purge; module load BWA/0.7.17"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index c0370c3cc76f7048a03382a6ee7985ec1085d9b5..d13f1f4e29bb5f84e9263827c6d8d53af5b6cf26 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17"
- executor = "sge"
+ executor = "psmn"
cpus = 4
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index d5851003aa4c3c95b34eb78de95e20ff17aee390..64df83d8e77c46983d6222d07bd2469feb7de114 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 86cc4bb7f3c6c553811f18ed64f03c003e4780ab..d2170da748d66e96d4a18b5ba45831c2a31a89c4 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 86cc4bb7f3c6c553811f18ed64f03c003e4780ab..d2170da748d66e96d4a18b5ba45831c2a31a89c4 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 60f60547c31e5c6fea842e3c798940a2ba6b98c5..91abd84d3bc366defa01ae35b5aa77f5d6d2f852 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index a8cd2991e8775c96045263645cf98079002275b1..1f2714a7c2ae69881900232ca269ef349fbffbb6 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index a8cd2991e8775c96045263645cf98079002275b1..1f2714a7c2ae69881900232ca269ef349fbffbb6 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index a6589845aa98db0b4f6eaa663246db2604eb210b..6e869185a8057c3bc9b0b9f6e13d422f3d7046bd 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/src/nf_modules/FastQC/fastqc_paired.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index a6589845aa98db0b4f6eaa663246db2604eb210b..6e869185a8057c3bc9b0b9f6e13d422f3d7046bd 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
index 00f2fafb921828b21fe18d57240b9a943dcd2fb9..6dad8c837205f64ee6021d18158598d88180a53e 100644
--- a/src/nf_modules/HTSeq/htseq.config
+++ b/src/nf_modules/HTSeq/htseq.config
@@ -11,7 +11,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config
index 0e8b5632af47704d2724db21d193860dc2286a91..95d38d09f62de6f60969259f03580c03c99a6490 100644
--- a/src/nf_modules/Kallisto/indexing.config
+++ b/src/nf_modules/Kallisto/indexing.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "sge"
+ executor = "psmn"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/Kallisto/mapping_paired.config b/src/nf_modules/Kallisto/mapping_paired.config
index 5a6102d99b7bb1d179eedee6f9a53cbd126517b3..5200ee092f0da1f47aa9eae6cb081cc145f26105 100644
--- a/src/nf_modules/Kallisto/mapping_paired.config
+++ b/src/nf_modules/Kallisto/mapping_paired.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "sge"
+ executor = "psmn"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config
index 5a6102d99b7bb1d179eedee6f9a53cbd126517b3..5200ee092f0da1f47aa9eae6cb081cc145f26105 100644
--- a/src/nf_modules/Kallisto/mapping_single.config
+++ b/src/nf_modules/Kallisto/mapping_single.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "sge"
+ executor = "psmn"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index 4685752be3d8e66da4e76aeffc82ce58d50389b3..70375472b84040885a9e827eabf05f09ff0bbb5b 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/src/nf_modules/MUSIC/peak_calling_single.config
@@ -14,7 +14,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$compute_mappability {
beforeScript = "module purge; module load MUSIC/6613c53"
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index c1bda95e70a612c7caf4825930e740faedd1c62d..a81a361f557ce60ae47308300bb77bffbb57040d 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/src/nf_modules/MultiQC/multiqc_paired.config
@@ -11,11 +11,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
@@ -25,7 +25,7 @@ profiles {
}
$multiqc {
beforeScript = "module purge; module load FastQC/1.0"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index c1bda95e70a612c7caf4825930e740faedd1c62d..a81a361f557ce60ae47308300bb77bffbb57040d 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -11,11 +11,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
@@ -25,7 +25,7 @@ profiles {
}
$multiqc {
beforeScript = "module purge; module load FastQC/1.0"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
index ddf93b6ec57c876681fc508a737b3287e20fdd61..52ead0dbba140ada3386f3f3f61b453a2c49b374 100644
--- a/src/nf_modules/RSEM/indexing.config
+++ b/src/nf_modules/RSEM/indexing.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 344ab1e30497454826a5e45537f0e8182fb8dc63..ad5c0388ec94ef981ad645900fe2bfc07ce125dc 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 344ab1e30497454826a5e45537f0e8182fb8dc63..ad5c0388ec94ef981ad645900fe2bfc07ce125dc 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$mapping_fastq {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index 066684006e4a04daef5caf26e45ba74878bb4ebf..cee59e8bc0d9cefaf7fbaff250113df002c64662 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 3b23601d9566ee96f034d14a798c6c8e08a6870f..040fee577b0ddd545443c55eeb5ec31ac2bf44f1 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index d1a8c503ace81d53fa5ff9cd382a435ac710e0cf..20dcdccf4af24e2af0a7cc39f5ef935b02b998cc 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
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
index 28b548efd5177e7457bd642b0c78198f2b48acd9..503d553953924d07b728142bd16f9e8ce8b33ca2 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$split_bam {
beforeScript = "module purge; module load SAMtools/1.7"
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index 128a4fef272aeb70993f5b614e0c34f901fc0c60..1c29984a4f8d2f283445c29ee624dcd7b38cf173 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$fastq_dump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
index c34e6d4e02ecb3bfd0b71f970edc746b3465e8a9..59760a7292738eda4897fe45d6968aa49a3bb77d 100644
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8"
- executor = "sge"
+ executor = "psmn"
cpus = 16
memory = "5GB"
time = "12h"
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
index c34e6d4e02ecb3bfd0b71f970edc746b3465e8a9..59760a7292738eda4897fe45d6968aa49a3bb77d 100644
--- a/src/nf_modules/UrQt/trimming_single.config
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8"
- executor = "sge"
+ executor = "psmn"
cpus = 16
memory = "5GB"
time = "12h"
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
index 46a86729f1367966225fcb37c5ef7f11070c7255..e08a434ad2b9f8e27cd95df6ce0324b776c69104 100644
--- a/src/nf_modules/UrQt/urqt.config
+++ b/src/nf_modules/UrQt/urqt.config
@@ -8,11 +8,11 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
- executor = "sge"
+ executor = "psmn"
cpus = 4
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index af234c0ceed670ed56edbaa322b8a35ca3781d06..ad9b4d285d8d896d423ad363a0ddc56aa29849b2 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index af234c0ceed670ed56edbaa322b8a35ca3781d06..ad9b4d285d8d896d423ad363a0ddc56aa29849b2 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index b103ecb46c51bc453b1a25022850da7c2803d179..6d5292d1043a94ccd84c90221e037ff00388cb10 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index b103ecb46c51bc453b1a25022850da7c2803d179..6d5292d1043a94ccd84c90221e037ff00388cb10 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -8,12 +8,12 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "sge"
+ executor = "psmn"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 0830a67ad8b1f6dd8eb993ec1c64b8ba94777f3e..cf0c5c7d2c20812516e325382cac02854b66dcfc 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$index_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 2e335ad319401bfa1a7e1422989a234e4faedecc..1303bd685a5a5b815f3fbc46e5983e632fabeecb 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$sort_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index d2182ba92d4c6f7c40d8490ceca973e06becaad3..c6d211c6d30602ac2a1d21d9ebf6db5375781989 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$split_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 69cff9971858dfba138ec5c4b335d566ece4235b..47ab19e1509b567d2b39af149d6a59be03f58be3 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -8,7 +8,7 @@ profiles {
}
}
}
- sge {
+ psmn {
process{
$dedup_sam {
beforeScript = "module purge; module load samblaster/0.1.24"
diff --git a/src/sge_modules b/src/psmn_modules
similarity index 100%
rename from src/sge_modules
rename to src/psmn_modules