Split version lines

e2ac42c7 · Gervaise Henry · e43e60c0 · e2ac42c7
Commit e2ac42c7 authored 4 years ago by Gervaise Henry
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,69 +40,57 @@ img_cache:
 collect:
  stage: versions
  script:
-    - >
+    - derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
-      derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
+    - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
-      derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
+    - echo ${dir}${derivaImg}_${derivaVar}.sif
-      echo ${dir}${derivaImg}_${derivaVar}.sif
+    - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
-      singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
+    - singularity run ${dir}${derivaImg}_${derivaVar}.sif bdbag --version > version_bdbag.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=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
-      pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
+    - echo ${dir}${pythonImg}_${pythonVar}.sif
-      pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
+    - singularity run ${dir}${pythonImg}_${pythonVar}.sif python3 --version > version_python.txt
-      echo ${dir}${pythonImg}_${pythonVar}.sif
+    - fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
-      singularity run ${dir}${pythonImg}_${pythonVar}.sif python3 --version > version_python.txt
+    - fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
-    - >
+    - echo ${dir}${fastqcImg}_${fastqcVar}.sif
-      fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
+    - singularity run ${dir}${fastqcImg}_${fastqcVar}.sif fastqc --version > version_fastqc.txt
-      fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
+    - seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
-      echo ${dir}${fastqcImg}_${fastqcVar}.sif
+    - seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
-      singularity run ${dir}${fastqcImg}_${fastqcVar}.sif fastqc --version > version_fastqc.txt
+    - echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
-    - >
+    - singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt &
-      seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
+    - trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
-      seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
+    - trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
-      echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
+    - echo ${dir}${trimgaloreImg}_${trimgaloreVar}.sif
-      singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt &
+    - 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)
-      trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
+    - seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
-      trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
+    - echo ${dir}${seqtkImg}_${seqtkVar}.sif
-      echo ${dir}${trimgaloreImg}_${trimgaloreVar}.sif
+    - singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt &
-      singularity run ${dir}${trimgaloreImg}_${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt
+    - rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
-    - >
+    - rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
-      seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
+    - echo ${dir}${rseqcImg}_${rseqcVar}.sif
-      seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
+    - singularity run ${dir}${rseqcImg}_${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
-      echo ${dir}${seqtkImg}_${seqtkVar}.sif
+    - hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
-      singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt &
+    - hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
-    - >
+    - echo ${dir}${hisatImg}_${hisatVar}.sif
-      rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
+    - singularity run ${dir}${hisatImg}_${hisatVar}.sif hisat2 --version > version_hisat2.txt
-      rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
+    - singularity run ${dir}${hisatImg}_${hisatVar}.sif samtools --version > version_samtools.txt
-      echo ${dir}${rseqcImg}_${rseqcVar}.sif
+    - picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
-      singularity run ${dir}${rseqcImg}_${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
+    - picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
-    - >
+    - echo ${dir}${picardImg}_${picardVar}.sif
-      hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
+    - singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt &
-      hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
+    - subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
-      echo ${dir}${hisatImg}_${hisatVar}.sif
+    - subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
-      singularity run ${dir}${hisatImg}_${hisatVar}.sif hisat2 --version > version_hisat2.txt
+    - echo ${dir}${subreadImg}_${subreadVar}.sif
-      singularity run ${dir}${hisatImg}_${hisatVar}.sif samtools --version > version_samtools.txt
+    - singularity run ${dir}${subreadImg}_${subreadVar}.sif featureCounts -v &> version_featurecounts.txt
-    - >
+    - singularity run ${dir}${subreadImg}_${subreadVar}.sif R --version > version_r.txt
-      picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
+    - deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
-      picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
+    - deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
-      echo ${dir}${picardImg}_${picardVar}.sif
+    - echo ${dir}${deeptoolsImg}_${deeptoolsVar}.sif
-      singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt &
+    - 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)
-      subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
+    - multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
-      subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
+    - echo ${dir}${multiqcImg}_${multiqcVar}.sif
-      echo ${dir}${subreadImg}_${subreadVar}.sif
+    - singularity run ${dir}${multiqcImg}_${multiqcVar}.sif multiqc --version > version_multiqc.txt
-      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)
-      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)
-      echo ${dir}${multiqcImg}_${multiqcVar}.sif
-      singularity run ${dir}${multiqcImg}_${multiqcVar}.sif multiqc --version > version_multiqc.txt
  artifacts:
    name: "$CI_JOB_NAME"
    when: always