diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 38a9d5934c217cecc9da212b0ad2c21be407260e..2456420f15bc94916a846a0a0d7d6c1b77508c8e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -40,69 +40,57 @@ img_cache: collect: stage: versions script: - - > - derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1) - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2) - echo ${dir}${derivaImg}_${derivaVar}.sif - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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}_${multiqcVar}.sif multiqc --version > version_multiqc.txt + - derivaImg=$(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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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) + - 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