add .signularity_in2p3 folder to fix lock problem in nf

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 {}

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {