From 670315f58b966b58036a3f5c175feea8a1245762 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 20 Apr 2020 16:21:48 +0200
Subject: [PATCH] nf_modules: switch psmn to singularity
---
src/.update_config.sh | 4 +-
src/nf_modules/bedtools/fasta_from_bed.config | 9 ++-
src/nf_modules/bowtie/indexing.config | 9 ++-
src/nf_modules/bowtie/mapping_paired.config | 9 ++-
src/nf_modules/bowtie/mapping_single.config | 9 ++-
src/nf_modules/bowtie2/indexing.config | 9 ++-
src/nf_modules/bowtie2/mapping_paired.config | 9 ++-
src/nf_modules/bowtie2/mapping_single.config | 9 ++-
src/nf_modules/bwa/indexing.config | 9 ++-
src/nf_modules/bwa/mapping_paired.config | 9 ++-
.../cutadapt/adaptor_removal_paired.config | 9 ++-
.../cutadapt/adaptor_removal_single.config | 9 ++-
.../cutadapt/trimming_paired.config | 9 ++-
.../cutadapt/trimming_single.config | 9 ++-
src/nf_modules/deeptools/bam_to_bigwig.config | 20 +++----
.../deeptools/compute_matrix.config | 9 ++-
src/nf_modules/deeptools/plot_profile.config | 9 ++-
src/nf_modules/fastp/fastp_paired.config | 9 ++-
src/nf_modules/fastp/fastp_single.config | 9 ++-
src/nf_modules/fastqc/fastqc_paired.config | 9 ++-
src/nf_modules/fastqc/fastqc_single.config | 9 ++-
src/nf_modules/hisat2/indexing.config | 9 ++-
src/nf_modules/htseq/htseq.config | 19 +++---
src/nf_modules/kallisto/indexing.config | 9 ++-
src/nf_modules/kallisto/mapping_paired.config | 9 ++-
src/nf_modules/kallisto/mapping_single.config | 9 ++-
src/nf_modules/macs2/peak_calling.config | 9 ++-
src/nf_modules/multiqc/multiqc_paired.config | 21 +++----
src/nf_modules/multiqc/multiqc_single.config | 21 +++----
.../music/peak_calling_single.config | 29 +++-------
src/nf_modules/rsem/indexing.config | 9 ++-
.../rsem/quantification_paired.config | 9 ++-
.../rsem/quantification_single.config | 9 ++-
src/nf_modules/sambamba/index_bams.config | 9 ++-
src/nf_modules/sambamba/sort_bams.config | 9 ++-
src/nf_modules/sambamba/split_bams.config | 9 ++-
src/nf_modules/samblaster/dedup_sams.config | 9 ++-
src/nf_modules/samtools/filter_bams.config | 9 ++-
src/nf_modules/samtools/index_bams.config | 9 ++-
src/nf_modules/samtools/sort_bams.config | 9 ++-
src/nf_modules/samtools/split_bams.config | 9 ++-
src/nf_modules/sratoolkit/fastqdump.config | 9 ++-
src/nf_modules/star/indexing.config | 9 ++-
src/nf_modules/star/mapping_paired.config | 9 ++-
src/nf_modules/star/mapping_single.config | 9 ++-
src/nf_modules/subread/subread.config | 19 +++---
src/nf_modules/urqt/trimming_paired.config | 9 ++-
src/nf_modules/urqt/trimming_single.config | 9 ++-
src/solution_RNASeq.config | 58 -------------------
49 files changed, 332 insertions(+), 228 deletions(-)
diff --git a/src/.update_config.sh b/src/.update_config.sh
index 080d000f..e8f4fc9b 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -25,4 +25,6 @@ fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
-
+# we update the psmn config to singularity
+fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n singularity.enabled = true\n singularity.cacheDir = "$baseDir/.singularity_psmn/"\n singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7642dec3..a59f2573 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fasta_from_bed {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bedtools_2.25.0"
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 0fa19189..10e15a38 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie_1.2.2"
+ container = "lbmc/bowtie:1.2.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index b29cc8de..591528f9 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+ container = "lbmc/bowtie:1.2.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index b29cc8de..591528f9 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+ container = "lbmc/bowtie:1.2.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2f37d692..9c3fc8ec 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 155b3668..140f6740 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 155b3668..140f6740 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 12adc8e6..03b85b1c 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bwa_0.7.17"
+ container = "lbmc/bwa:0.7.17"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 7fce44a3..73da4757 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bwa_0.7.17"
+ container = "lbmc/bwa:0.7.17"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 30b344cd..6def9752 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 30b344cd..6def9752 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 397c7f5c..f813ab4f 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 397c7f5c..f813ab4f 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 6d26a3e5..81fac55d 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -28,21 +28,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: bam_to_bigwig {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "deeptools/3.0.2"
+ container = "lbmc/deeptools:3.0.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 5a8c4135..d020de9a 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: compute_matrix {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+ container = "lbmc/deeptools:3.0.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 67b36ba4..5dec8218 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: plot_profile {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+ container = "lbmc/deeptools:3.0.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index becedca3..68f316c5 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastp_0.19.7"
+ container = "lbmc/fastp:0.19.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index becedca3..68f316c5 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastp_0.19.7"
+ container = "lbmc/fastp:0.19.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index eddcc94b..98e4c1df 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+ container = "lbmc/fastqc:0.11.5"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index eddcc94b..98e4c1df 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+ container = "lbmc/fastqc:0.11.5"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index e726418f..ba2915cb 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/hisat2_2.1.0"
+ container = "lbmc/hisat2:2.1.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 40f27a3a..72d14bec 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -28,20 +28,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: counting {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "htseq/0.11.2"
+ container = "lbmc/htseq:0.11.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 14dd1ade..ef535de8 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 7fdd1dcd..d4bc1680 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 7fdd1dcd..d4bc1680 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 7c4c8500..2d250ef0 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: peak_calling {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/macs2_2.1.2"
+ container = "lbmc/macs2:2.1.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index d0202652..68d4b992 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -29,22 +29,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1.70
- pollInterval = "60sec"
- queue = "monointeldeb128"
- }
- withName: multiqc {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.7"
+ container = "lbmc/multiqc:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 301dde8b..7dbea6c6 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -28,22 +28,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1.70
- pollInterval = "60sec"
- queue = "monointeldeb128"
- }
- withName: multiqc {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.7"
+ container = "lbmc/multiqc:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 0372788c..19d8002b 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -36,30 +36,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: compute_mappability {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/music_6613c53"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: music_preprocessing {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "music/6613c53"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: music_computation{
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "music/6613c53"
+ container = "lbmc/music:6613c53"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index c2c06001..9a3d570c 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index fd73ae66..5371df44 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index fd73ae66..5371df44 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index c3d12b70..5e710fca 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 1db926f7..4a551993 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 1ec31c3e..86934b58 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: split_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 10c1649e..c7f2dc36 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: dedup_sam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samblaster_0.1.24"
+ container = "lbmc/sambamba:0.6.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 46933f1d..17e7fefd 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: filter_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 438f8379..234119a0 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 81371fb5..dd020ab0 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 837fe88d..cd34b085 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: split_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 4c651697..cc260862 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastq_dump {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
+ container = "lbmc/sratoolkit:2.8.2"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index cef16406..490aea02 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 6f8f8048..e737ad12 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 6f8f8048..e737ad12 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index ef2aa7e5..9ddbadb0 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -28,20 +28,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: counting {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "subread/1.6.4"
+ container = "lbmc/subread:1.6.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 87f7f7f9..a7dd1111 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index c2b5757e..a2719bd3 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index d17bc417..77142cab 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -52,64 +52,6 @@ profiles {
}
}
psmn{
- process{
- withName: adaptor_removal {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/urqt_d62c1f8"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
-
- }
- withName: fasta_from_bed {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bedtools_2.25.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- psmn_singularity{
singularity.enabled = true
singularity.cacheDir = "$baseDir/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
--
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