in2p3 test: make singularity default for ccin2p3

src/kallisto_index.pbs

@@ -24,6 +24,6 @@ PIPELINE=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.nf
 # change to your project / pipeline !
 CONFIG=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.config
 
-${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3_singularity \
+${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
 --fasta "${SCRATCH}/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
--w "${SCRATCH}" -ansi-log false
+-w "${SCRATCH}"

src/nf_modules/kallisto/indexing.config

@@ -33,7 +33,7 @@ profiles {
       }
     }
   }
-  ccin2p3 {
+  ccin2p3_conda {
     process{
       withName: index_fasta {
         beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
@@ -49,19 +49,18 @@ profiles {
       }
     }
   }
-  ccin2p3_singularity {
+  ccin2p3 {
     singularity.enabled = true
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "export SINGULARITY_BIND=\"/sps,/scratch:/var/singularity/mnt/\""
         container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
-        -o /sps/lbmc/lmodolo/logs/ -e /sps/lbmc/lmodolo/logs/ -M laurent.modolo@ens-lyon.fr -m beas"
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
         queue = 'huge'
       }

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
@@ -21,10 +20,8 @@ process index_fasta {
 
   script:
 """
-pwd
 kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
 2> ${fasta.baseName}_kallisto_report.txt
-pwd
 """
 }