From 323124186c5616f58e12c8ffe6f6abcc5a18c4ae Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 27 Nov 2019 17:48:37 +0100
Subject: [PATCH] add .signularity_in2p3 folder to fix lock problem in nf
---
src/.update_config.sh | 3 ++-
src/nf_modules/bedtools/fasta_from_bed.config | 2 +-
src/nf_modules/bowtie/indexing.config | 2 +-
src/nf_modules/bowtie/mapping_paired.config | 2 +-
src/nf_modules/bowtie/mapping_single.config | 2 +-
src/nf_modules/bowtie2/indexing.config | 2 +-
src/nf_modules/bowtie2/mapping_paired.config | 2 +-
src/nf_modules/bowtie2/mapping_single.config | 2 +-
src/nf_modules/bwa/indexing.config | 2 +-
src/nf_modules/bwa/mapping_paired.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_paired.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_single.config | 2 +-
src/nf_modules/cutadapt/trimming_paired.config | 2 +-
src/nf_modules/cutadapt/trimming_single.config | 2 +-
src/nf_modules/deeptools/bam_to_bigwig.config | 2 +-
src/nf_modules/deeptools/compute_matrix.config | 2 +-
src/nf_modules/deeptools/plot_profile.config | 2 +-
src/nf_modules/fastp/fastp_paired.config | 2 +-
src/nf_modules/fastp/fastp_single.config | 2 +-
src/nf_modules/fastqc/fastqc_paired.config | 2 +-
src/nf_modules/fastqc/fastqc_single.config | 2 +-
src/nf_modules/hisat2/indexing.config | 2 +-
src/nf_modules/hisat2/mapping_paired.config | 2 +-
src/nf_modules/hisat2/mapping_single.config | 2 +-
src/nf_modules/htseq/htseq.config | 2 +-
src/nf_modules/kallisto/indexing.config | 2 +-
src/nf_modules/kallisto/mapping_paired.config | 2 +-
src/nf_modules/kallisto/mapping_single.config | 2 +-
src/nf_modules/macs2/peak_calling.config | 2 +-
src/nf_modules/multiqc/multiqc_paired.config | 2 +-
src/nf_modules/multiqc/multiqc_single.config | 2 +-
src/nf_modules/music/peak_calling_single.config | 2 +-
src/nf_modules/rsem/indexing.config | 2 +-
src/nf_modules/rsem/quantification_paired.config | 2 +-
src/nf_modules/rsem/quantification_single.config | 2 +-
src/nf_modules/sambamba/index_bams.config | 2 +-
src/nf_modules/sambamba/sort_bams.config | 2 +-
src/nf_modules/sambamba/split_bams.config | 2 +-
src/nf_modules/samblaster/dedup_sams.config | 2 +-
src/nf_modules/samtools/filter_bams.config | 2 +-
src/nf_modules/samtools/index_bams.config | 2 +-
src/nf_modules/samtools/sort_bams.config | 2 +-
src/nf_modules/samtools/split_bams.config | 2 +-
src/nf_modules/sratoolkit/fastqdump.config | 2 +-
src/nf_modules/star/indexing.config | 2 +-
src/nf_modules/star/mapping_paired.config | 2 +-
src/nf_modules/star/mapping_single.config | 2 +-
src/nf_modules/subread/subread.config | 2 +-
src/nf_modules/urqt/trimming_paired.config | 2 +-
src/nf_modules/urqt/trimming_single.config | 2 +-
50 files changed, 51 insertions(+), 50 deletions(-)
diff --git a/src/.update_config.sh b/src/.update_config.sh
index ffb76502..c39630d9 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -5,11 +5,12 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container =
fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
# update singularity config
-fd ".*config" -E "nf_modules" src/ -x perl -0776pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
# update in2p3 config
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n ccin2p3 {\n singularity.enabled = true\n singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
fd ".*config" src/ -x perl -pe 's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g' -i {}
+fd ".*config" src/ -x perl -0777pe 's|singularity.cacheDir = "/sps/lbmc/common/singularity/"|singularity.cacheDir = "\$baseDir/.src/singularity_in2p3/"|mg' -i {}
# we remove the ccin2p3_conda section
fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p3 {\n|\n ccin2p3 {\n|msg" -i {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 3372d452..46e5e2fa 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fasta_from_bed {
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 32db140e..8dfb6d77 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 4aa916d0..b843424d 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 4aa916d0..b843424d 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 0fcb8507..45ea20f3 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 7111d239..ea515a40 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 7111d239..ea515a40 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index b852e153..b8336aeb 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index b493b5f4..6fba33f1 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index c6ad6528..b0797ffc 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index c6ad6528..b0797ffc 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index edbee713..2acbf677 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index edbee713..2acbf677 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index a30225b8..bc680b8d 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -55,7 +55,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 2e178044..0cf27149 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: compute_matrix {
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index cceb4746..ec20c4c8 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: plot_profile {
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index a9129ddb..42656ec4 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index a9129ddb..42656ec4 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index e01fa5f5..b7a74efe 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastqc_fastq {
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index e01fa5f5..b7a74efe 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastqc_fastq {
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 6322661b..cfe8eab3 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 860fc2f7..5aa86481 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 860fc2f7..5aa86481 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 52c8ae86..25d2ff69 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -53,7 +53,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 9bbba3d6..303abd88 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 5e1784b9..a6c4b720 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 5e1784b9..a6c4b720 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 747f26bb..10980bed 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: peak_calling {
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 0b220310..689a8b1b 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -58,7 +58,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_fastqc {
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 80ecd7fd..4d69a356 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -57,7 +57,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_fastqc {
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 01261907..c4e6cdfc 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -71,7 +71,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: compute_mappability {
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index be6169e2..446ebb61 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 97502ecd..11e4e349 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 97502ecd..11e4e349 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 95cb2371..7bb232ab 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 3dd3273b..1c1772dd 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index c774bd7f..9c33cef9 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: split_bam {
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index cd17da01..81345968 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: dedup_sam {
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index a909fd16..3c920d2a 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: filter_bam {
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 1ab10017..5e02b240 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index d3bbfa8b..bca093bf 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 56b1eafc..71903753 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: split_bam {
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index e01b71bc..bdeff96d 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_dump {
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index 3e4017b9..7046e632 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index c2de5c50..29ea1f2c 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index c2de5c50..29ea1f2c 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index f0153ffa..0e8b9a6c 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -53,7 +53,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 4d8b855f..e7c8b6b1 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index b8b8fc16..c8f16ba6 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
--
GitLab