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 b271cfbe..57a4299e 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 4c8e39f2..b1954161 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 f4b744b7..6e198953 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 607bda58..4f9e6976 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 c0370c3c..d13f1f4e 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 d5851003..64df83d8 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 86cc4bb7..d2170da7 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 86cc4bb7..d2170da7 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 60f60547..91abd84d 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 a8cd2991..1f2714a7 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 a8cd2991..1f2714a7 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 a6589845..6e869185 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 a6589845..6e869185 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 00f2fafb..6dad8c83 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 0e8b5632..95d38d09 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 5a6102d9..5200ee09 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 5a6102d9..5200ee09 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 4685752b..70375472 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 c1bda95e..a81a361f 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 c1bda95e..a81a361f 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 ddf93b6e..52ead0db 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 344ab1e3..ad5c0388 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 344ab1e3..ad5c0388 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 06668400..cee59e8b 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 3b23601d..040fee57 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 d1a8c503..20dcdccf 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 28b548ef..503d5539 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 128a4fef..1c29984a 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 c34e6d4e..59760a72 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 c34e6d4e..59760a72 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 46a86729..e08a434a 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 af234c0c..ad9b4d28 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 af234c0c..ad9b4d28 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 b103ecb4..6d5292d1 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 b103ecb4..6d5292d1 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 0830a67a..cf0c5c7d 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 2e335ad3..1303bd68 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 d2182ba9..c6d211c6 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 69cff997..47ab19e1 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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