nf modules: adapt ccin2p3 profile to use singularity

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"