From 99eb87053a5094715087fd396dd355794cd23fe0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 7 May 2019 14:35:30 +0200
Subject: [PATCH] nf_modules: update ccin2p3 config
---
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 | 18 +++++----
.../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/hisat2/mapping_paired.config | 9 +++--
src/nf_modules/hisat2/mapping_single.config | 9 +++--
src/nf_modules/htseq/htseq.config | 22 ++++++-----
src/nf_modules/kallisto/indexing.config | 16 +-------
src/nf_modules/kallisto/mapping_paired.config | 9 +++--
src/nf_modules/kallisto/mapping_single.config | 9 +++--
src/nf_modules/macs2/peak_calling.config | 11 +++---
src/nf_modules/multiqc/multiqc_paired.config | 18 +++++----
src/nf_modules/multiqc/multiqc_single.config | 18 +++++----
.../music/peak_calling_single.config | 38 +++++++++++++++++++
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/urqt/trimming_paired.config | 9 +++--
src/nf_modules/urqt/trimming_single.config | 9 +++--
45 files changed, 277 insertions(+), 206 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index eed73258..17dee4b1 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fasta_from_bed {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bedtools/2.25.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 10c4ac96..627cc943 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index f531d0dc..598b99a1 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index f531d0dc..598b99a1 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 80de2148..966b7a9f 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 44adb9a5..5c975a8c 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 44adb9a5..5c975a8c 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index a6e6d9fe..eeb59fad 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index d583ff1c..7b964120 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index f7d0ebbd..6fb8ea64 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index f7d0ebbd..6fb8ea64 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 35f0963e..0aef1942 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 35f0963e..0aef1942 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 75f8575f..30b3b0f9 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -55,28 +55,30 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
process{
withName: bam_to_bigwig {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index f20b5a82..bb3d987f 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: compute_matrix {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index d31d37ab..de2276e8 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: plot_profile {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 93ebee83..b93eccd1 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 93ebee83..b93eccd1 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index e6404b8f..a74fb951 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index e6404b8f..a74fb951 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 3292c316..c56f1819 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 3def2911..23a4acc5 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 3def2911..23a4acc5 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index f3667f4f..ec072e0b 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -34,7 +34,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
- withName: trimming {
+ withName: counting {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "htseq/0.11.2"
executor = "sge"
@@ -49,26 +49,28 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
- withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/htseq/0.11.2/:/usr/bin:$PATH"
+ withName: counting {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b51369e1..501daa09 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -34,20 +34,6 @@ profiles {
}
}
ccin2p3 {
- process{
- withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = 'huge'
- }
- }
- }
- ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
@@ -57,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o /sps/lbmc/lmodolo/logs/ -e /sps/lbmc/lmodolo/logs/"
+ -o ~/logs/ -e ~/logs/"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 48ee3405..bfbbb6b2 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 48ee3405..bfbbb6b2 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 2eaed2e7..3538315e 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -35,16 +35,17 @@ profiles {
}
ccin2p3 {
process{
- withName: peak_calling {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/macs2/2.1.2/:/usr/bin:$PATH"
+ withName: mapping_fastq {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 3824f623..51afdbb3 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -58,26 +58,28 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
withName: multiqc {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/multiqc/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index b451a30c..bde67e34 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -57,26 +57,28 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
withName: multiqc {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/multiqc/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 1ae50627..bd7036b0 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -104,5 +104,43 @@ profiles {
time = "24h"
}
}
+ process{
+ withName: compute_mappability {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_preprocessing {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_computation {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index a85d7233..03ee920b 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 58baa5c6..4f859c2e 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 58baa5c6..4f859c2e 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index dd88348a..335f0fa6 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index fe605cf4..6865c9a3 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 087a0dd5..740c51e0 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 883cbe69..951d6f87 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: dedup_sam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samblaster/0.1.24/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index c8bab8db..f2f899b6 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: filter_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 89c223b4..d5336bb0 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 6d30cc5b..8d1153d2 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 9cd8b166..72501731 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 8c1087e5..664482e0 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastq_dump {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sratoolkit/2.8.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 32ccee84..1b250b39 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/urqt/d62c1f8/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index d4c9b3ac..b107cf22 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/urqt/d62c1f8/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
--
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