From 6cccaa962ece13b51a77566ca1cb0a3140909269 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 20 May 2019 17:10:26 +0200
Subject: [PATCH] nf modules: adapt ccin2p3 profile to use singularity
---
src/nf_modules/bedtools/fasta_from_bed.config | 4 +--
src/nf_modules/bowtie/indexing.config | 2 +-
src/nf_modules/bowtie/mapping_paired.config | 4 +--
src/nf_modules/bowtie/mapping_single.config | 4 +--
src/nf_modules/bowtie2/indexing.config | 2 +-
src/nf_modules/bowtie2/mapping_paired.config | 4 +--
src/nf_modules/bowtie2/mapping_single.config | 4 +--
src/nf_modules/bwa/indexing.config | 2 +-
src/nf_modules/bwa/mapping_paired.config | 4 +--
.../cutadapt/adaptor_removal_paired.config | 4 +--
.../cutadapt/adaptor_removal_single.config | 4 +--
.../cutadapt/trimming_paired.config | 4 +--
.../cutadapt/trimming_single.config | 4 +--
.../deeptools/compute_matrix.config | 4 +--
src/nf_modules/deeptools/plot_profile.config | 4 +--
src/nf_modules/fastp/fastp_paired.config | 4 +--
src/nf_modules/fastp/fastp_single.config | 4 +--
src/nf_modules/fastqc/fastqc_paired.config | 4 +--
src/nf_modules/fastqc/fastqc_single.config | 4 +--
src/nf_modules/hisat2/indexing.config | 2 +-
src/nf_modules/hisat2/mapping_paired.config | 4 +--
src/nf_modules/hisat2/mapping_single.config | 4 +--
src/nf_modules/htseq/htseq.config | 15 +++++++++--
src/nf_modules/kallisto/mapping_paired.config | 2 +-
src/nf_modules/kallisto/mapping_single.config | 2 +-
src/nf_modules/macs2/peak_calling.config | 4 +--
src/nf_modules/multiqc/multiqc_paired.config | 15 +++++++++--
src/nf_modules/multiqc/multiqc_single.config | 15 +++++++++--
.../music/peak_calling_single.config | 26 +++++++++++++++++--
src/nf_modules/rsem/indexing.config | 2 +-
.../rsem/quantification_paired.config | 4 +--
.../rsem/quantification_single.config | 4 +--
src/nf_modules/sambamba/index_bams.config | 4 +--
src/nf_modules/sambamba/sort_bams.config | 5 ++--
src/nf_modules/sambamba/split_bams.config | 4 +--
src/nf_modules/samblaster/dedup_sams.config | 4 +--
src/nf_modules/samtools/filter_bams.config | 4 +--
src/nf_modules/samtools/index_bams.config | 4 +--
src/nf_modules/samtools/sort_bams.config | 4 +--
src/nf_modules/samtools/split_bams.config | 4 +--
src/nf_modules/sratoolkit/fastqdump.config | 4 +--
src/nf_modules/urqt/trimming_paired.config | 4 +--
src/nf_modules/urqt/trimming_single.config | 4 +--
43 files changed, 135 insertions(+), 79 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 220cdce3..41c1dac9 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fasta_from_bed {
+ container = "/sps/lbmc/common/singularity/bedtools:2.25.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index e1b0262d..73217f9a 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index d24ba5d8..44ab8bcb 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index d24ba5d8..44ab8bcb 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 98b7cdac..20487563 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 7d8e543f..7874ae45 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 7d8e543f..7874ae45 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 89574aa8..72274ad4 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity//bwa:0.7.17.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 4f013608..a3e5c628 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 7317fb7b..e58c385a 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: adaptor_removal {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 7317fb7b..e58c385a 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: adaptor_removal {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index f201a571..9b49fcee 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index f201a571..9b49fcee 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 66be28dd..fb1cd048 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: compute_matrix {
+ container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index bb1feb2e..08d20977 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: plot_profile {
+ container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 67af9be5..7d9c83e4 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastp_fastq {
+ container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 67af9be5..7d9c83e4 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastp_fastq {
+ container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 70c9b996..6e9dcaf7 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastqc_fastq {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 70c9b996..6e9dcaf7 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastqc_fastq {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index c3784d31..6d39e60a 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 993ef10b..97b4807d 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 993ef10b..97b4807d 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 7349c5f0..09b368ae 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -78,8 +78,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ 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: counting {
+ container = "/sps/lbmc/common/singularity/htseq:0.11.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 2599af59..801dfdc1 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -53,7 +53,7 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withName: mapping_fastq {
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 2599af59..801dfdc1 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -53,7 +53,7 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withName: mapping_fastq {
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index d5223cd1..93697c70 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: peak_calling {
+ container = "/sps/lbmc/common/singularity/macs2:2.1.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 813b55e2..86ead2c4 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -87,8 +87,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_fastqc {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ 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: multiqc {
+ container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 304ea3e0..e296853f 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -86,8 +86,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_fastqc {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ 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: multiqc {
+ container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 64a55bd0..972de3d7 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -112,8 +112,30 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: compute_mappability {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ 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 {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ 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 {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 1149d299..b9de2536 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 35193330..03152cca 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 35193330..03152cca 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 7055c98c..cb3d4308 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: index_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 2ccdc387..de2eb6e8 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -64,6 +64,7 @@ profiles {
cpus = 1
queue = 'huge'
}
+
}
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 57346f10..74dd96d0 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: split_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 6911ff93..a47c35ac 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: dedup_sam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 0116e7c6..dfc5d68f 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: filter_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index dfab8d3d..3c0e876c 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: index_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 45c69f8a..690dc903 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index f03bc1a8..6afd8880 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: split_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 1538b1a0..6abc3955 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_dump {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 2073efc2..976921f2 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index e82bd35f..99fb7d94 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
--
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