From fa486dc61ea8bcd3392f216684730dfd5c16111e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 15:53:18 +0200
Subject: [PATCH] nf config: rename sge to psmn
---
.gitmodules | 2 +-
doc/TP_experimental_biologists.md | 12 ++++++------
src/nf_modules/BEDtools/fasta_from_bed.config | 4 ++--
src/nf_modules/BWA/indexing.config | 4 ++--
src/nf_modules/BWA/mapping_paired.config | 4 ++--
src/nf_modules/Bowtie/indexing.config | 2 +-
src/nf_modules/Bowtie/mapping_paired.config | 2 +-
src/nf_modules/Bowtie/mapping_single.config | 2 +-
src/nf_modules/Bowtie2/indexing.config | 2 +-
src/nf_modules/Bowtie2/mapping_paired.config | 2 +-
src/nf_modules/Bowtie2/mapping_single.config | 2 +-
src/nf_modules/FastQC/fastqc_paired.config | 4 ++--
src/nf_modules/FastQC/fastqc_single.config | 4 ++--
src/nf_modules/HTSeq/htseq.config | 2 +-
src/nf_modules/Kallisto/indexing.config | 4 ++--
src/nf_modules/Kallisto/mapping_paired.config | 4 ++--
src/nf_modules/Kallisto/mapping_single.config | 4 ++--
src/nf_modules/MUSIC/peak_calling_single.config | 2 +-
src/nf_modules/MultiQC/multiqc_paired.config | 6 +++---
src/nf_modules/MultiQC/multiqc_single.config | 6 +++---
src/nf_modules/RSEM/indexing.config | 2 +-
src/nf_modules/RSEM/quantification_paired.config | 2 +-
src/nf_modules/RSEM/quantification_single.config | 2 +-
src/nf_modules/SAMtools/filter_bams.config | 2 +-
src/nf_modules/SAMtools/index_bams.config | 2 +-
src/nf_modules/SAMtools/sort_bams.config | 2 +-
src/nf_modules/SAMtools/split_bams.config | 2 +-
src/nf_modules/SRAtoolkit/fastqdump.config | 4 ++--
src/nf_modules/UrQt/trimming_paired.config | 4 ++--
src/nf_modules/UrQt/trimming_single.config | 4 ++--
src/nf_modules/UrQt/urqt.config | 4 ++--
.../cutadapt/adaptor_removal_paired.config | 4 ++--
.../cutadapt/adaptor_removal_single.config | 4 ++--
src/nf_modules/cutadapt/trimming_paired.config | 4 ++--
src/nf_modules/cutadapt/trimming_single.config | 4 ++--
src/nf_modules/sambamba/index_bams.config | 2 +-
src/nf_modules/sambamba/sort_bams.config | 2 +-
src/nf_modules/sambamba/split_bams.config | 2 +-
src/nf_modules/samblaster/dedup_sams.config | 2 +-
src/{sge_modules => psmn_modules} | 0
40 files changed, 64 insertions(+), 64 deletions(-)
rename src/{sge_modules => psmn_modules} (100%)
diff --git a/.gitmodules b/.gitmodules
index b271cfb..57a4299 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 4c8e39f..b195416 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 f4b744b..6e19895 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 607bda5..4f9e697 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 c0370c3..d13f1f4 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 d585100..64df83d 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 86cc4bb..d2170da 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 86cc4bb..d2170da 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 60f6054..91abd84 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 a8cd299..1f2714a 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 a8cd299..1f2714a 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 a658984..6e86918 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 a658984..6e86918 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 00f2faf..6dad8c8 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 0e8b563..95d38d0 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 5a6102d..5200ee0 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 5a6102d..5200ee0 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 4685752..7037547 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 c1bda95..a81a361 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 c1bda95..a81a361 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 ddf93b6..52ead0d 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 344ab1e..ad5c038 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 344ab1e..ad5c038 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 0666840..cee59e8 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 3b23601..040fee5 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 d1a8c50..20dcdcc 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 28b548e..503d553 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 128a4fe..1c29984 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 c34e6d4..59760a7 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 c34e6d4..59760a7 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 46a8672..e08a434 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 af234c0..ad9b4d2 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 af234c0..ad9b4d2 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 b103ecb..6d5292d 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 b103ecb..6d5292d 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 0830a67..cf0c5c7 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 2e335ad..1303bd6 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 d2182ba..c6d211c 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 69cff99..47ab19e 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
--
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