add .signularity_in2p3 folder to fix lock problem in nf

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {

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 {