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Commit 469ef281 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Put sif names together

parent 27f3b44f
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2 merge requests!76Develop,!71Seqwho
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.gitlab-ci.yml
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...@@ -41,55 +41,66 @@ collect: ...@@ -41,55 +41,66 @@ collect:
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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}-${derivaVar}.sif img=$(echo ${dir}${derivaImg}-${derivaVar}.sif)
singularity run ${dir}${derivaImg}-${derivaVar}.sif deriva-download-cli --version > version_deriva.txt singularity run ${img} deriva-download-cli --version > version_deriva.txt
singularity run ${dir}${derivaImg}-${derivaVar}.sif bdbag --version > version_bdbag.txt singularity run ${img} bdbag --version > version_bdbag.txt
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pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1) 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) pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${pythonImg}-${pythonVar}.sif python3 --version > version_python.txt img=$(${dir}${pythonImg}-${pythonVar}.sif)
singularity run ${img} python3 --version > version_python.txt
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fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1) 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) fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${fastqcImg}-${fastqcVar}.sif fastqc --version > version_fastqc.txt img=$(echo ${dir}${fastqcImg}-${fastqcVar}.sif)
singularity run ${img} fastqc --version > version_fastqc.txt
- > - >
seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1) 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) seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${seqwhoImg}-${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt img=$(${dir}${seqwhoImg}-${seqwhoVar}.sif)
singularity run ${img} seqwho.py -h | grep -o Version.* > version_seqwho.txt
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trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1) trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | 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)
singularity run ${dir}${trimgaloreImg}-${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt img=$(echo ${dir}${trimgaloreImg}-${trimgaloreVar}.sif)
singularity run ${img} trim_galore --version > version_trimgalore.txt
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seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1) 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) seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${seqtkImg}-${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt& img=$(echo ${dir}${seqtkImg}-${seqtkVar}.sif)
singularity run ${img} seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
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rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1) 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) rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${rseqcImg}-${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt img=$(echo ${dir}${rseqcImg}-${rseqcVar}.sif)
singularity run ${img} infer_experiment.py --version > version_rseqc.txt
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hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1) 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) hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${hisatImg}-${hisatVar}.sif hisat2 --version > version_hisat2.txt img=$(echo ${dir}${hisatImg}-${hisatVar}.sif)
singularity run ${dir}${hisatImg}-${hisatVar}.sif samtools --version > version_samtools.txt singularity run ${img} hisat2 --version > version_hisat2.txt
singularity run ${img} samtools --version > version_samtools.txt
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picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1) 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) picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${picardImg}-${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt& img=$(echo ${dir}${picardImg}-${picardVar}.sif)
singularity run ${img} java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
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subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1) subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | 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)
singularity run ${dir}${subreadImg}-${subreadVar}.sif featureCounts -v &> version_featurecounts.txt img=$(echo ${dir}${subreadImg}-${subreadVar}.sif)
singularity run ${dir}${subreadImg}-${subreadVar}.sif R --version > version_r.txt singularity run ${img} featureCounts -v &> version_featurecounts.txt
singularity run ${img} R --version > version_r.txt
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deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1) deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | 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)
singularity run ${dir}${deeptoolsImg}-${deeptoolsVar}.sif deeptools --version > version_deeptools.txt img=$(echo ${dir}${deeptoolsImg}-${deeptoolsVar}.sif)
singularity run ${img} deeptools --version > version_deeptools.txt
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multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1) 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) multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
singularity run ${dir}${multiqcImg}-${multiqcVar}.sif multiqc --version > version_multiqc.txt img=$(echo ${dir}${multiqcImg}-${multiqcVar}.sif)
singularity run ${img} multiqc --version > version_multiqc.txt
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
......
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