kallisto: config for in2p3, add /usr/bin to path

src/nf_modules/kallisto/indexing.config

@@ -3,7 +3,7 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withName: index_fasta {
+      withNamek index_fasta {
         container = "kallisto:0.44.0"
         cpus = 4
       }
@@ -36,7 +36,7 @@ profiles {
   ccin2p3 {
     process{
       withName: index_fasta {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:$PATH"
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"

src/nf_modules/kallisto/indexing.nf

@@ -10,7 +10,6 @@ Channel
 process index_fasta {
   tag "$fasta.baseName"
   publishDir "results/mapping/index/", mode: 'copy'
-  echo true
 
   input:
     file fasta from fasta_file
@@ -21,7 +20,6 @@ process index_fasta {
 
   script:
 """
-pwd
 kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
 2> ${fasta.baseName}_kallisto_report.txt
 """