nf modules: adapt ccin2p3 profile to use singularity

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"

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"

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"