Try echo sif before run

.gitlab-ci.yml

@@ -41,66 +41,66 @@ collect:
     - >
       derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
       derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${derivaImg}-${derivaVar}.sif)
-      singularity run "${img}" deriva-download-cli --version > version_deriva.txt
-      singularity run "${img}" bdbag --version > version_bdbag.txt
+      echo ${dir}${derivaImg}-${derivaVar}.sif
+      singularity run ${dir}${derivaImg}-${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
+      singularity run ${dir}${derivaImg}-${derivaVar}.sif bdbag --version > version_bdbag.txt
     - >
       pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
       pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(${dir}${pythonImg}-${pythonVar}.sif)
-      singularity run "${img}" python3 --version > version_python.txt
+      echo ${dir}${pythonImg}-${pythonVar}.sif
+      singularity run ${dir}${pythonImg}-${pythonVar}.sif python3 --version > version_python.txt
     - >
       fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
       fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${fastqcImg}-${fastqcVar}.sif)
-      singularity run "${img}" fastqc --version > version_fastqc.txt
+      echo ${dir}${fastqcImg}-${fastqcVar}.sif
+      singularity run ${dir}${fastqcImg}-${fastqcVar}.sif fastqc --version > version_fastqc.txt
     - >
       seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
       seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(${dir}${seqwhoImg}-${seqwhoVar}.sif)
-      singularity run "${img}" seqwho.py -h | grep -o Version.* > version_seqwho.txt
+      echo ${dir}${seqwhoImg}-${seqwhoVar}.sif
+      singularity run ${dir}${seqwhoImg}-${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt
     - >
       trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
       trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${trimgaloreImg}-${trimgaloreVar}.sif)
-      singularity run "${img}" trim_galore --version > version_trimgalore.txt
+      echo ${dir}${trimgaloreImg}-${trimgaloreVar}.sif
+      singularity run ${dir}${trimgaloreImg}-${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt
     - >
       seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
       seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${seqtkImg}-${seqtkVar}.sif)
-      singularity run "${img}" seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
+      echo ${dir}${seqtkImg}-${seqtkVar}.sif
+      singularity run ${dir}${seqtkImg}-${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
     - >
       rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
       rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${rseqcImg}-${rseqcVar}.sif)
-      singularity run "${img}" infer_experiment.py --version > version_rseqc.txt
+      echo ${dir}${rseqcImg}-${rseqcVar}.sif
+      singularity run ${dir}${rseqcImg}-${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
     - >
       hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
       hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${hisatImg}-${hisatVar}.sif)
-      singularity run "${img}" hisat2 --version > version_hisat2.txt
-      singularity run "${img}" samtools --version > version_samtools.txt
+      echo ${dir}${hisatImg}-${hisatVar}.sif
+      singularity run ${dir}${hisatImg}-${hisatVar}.sif hisat2 --version > version_hisat2.txt
+      singularity run ${dir}${hisatImg}-${hisatVar}.sif samtools --version > version_samtools.txt
     - >
       picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
       picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${picardImg}-${picardVar}.sif)
-      singularity run "${img}" java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
+      echo ${dir}${picardImg}-${picardVar}.sif
+      singularity run ${dir}${picardImg}-${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
     - >
       subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
       subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${subreadImg}-${subreadVar}.sif)
-      singularity run "${img}" featureCounts -v &> version_featurecounts.txt
-      singularity run "${img}" R --version > version_r.txt
+      echo ${dir}${subreadImg}-${subreadVar}.sif
+      singularity run ${dir}${subreadImg}-${subreadVar}.sif featureCounts -v &> version_featurecounts.txt
+      singularity run ${dir}${subreadImg}-${subreadVar}.sif R --version > version_r.txt
     - >
       deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
       deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${deeptoolsImg}-${deeptoolsVar}.sif)
-      singularity run "${img}" deeptools --version > version_deeptools.txt
+      echo ${dir}${deeptoolsImg}-${deeptoolsVar}.sif
+      singularity run ${dir}${deeptoolsImg}-${deeptoolsVar}.sif deeptools --version > version_deeptools.txt
     - >
       multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1)
       multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
-      img=$(echo ${dir}${multiqcImg}-${multiqcVar}.sif)
-      singularity run "${img}" multiqc --version > version_multiqc.txt
+      echo ${dir}${multiqcImg}-${multiqcVar}.sif
+      singularity run ${dir}${multiqcImg}-${multiqcVar}.sif multiqc --version > version_multiqc.txt
   artifacts:
     name: "$CI_JOB_NAME"
     when: always