diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 8d2c49d64b1e83ac14e7cd54c1410014d4148e0c..dffe38a619e4c05459724e4d5c2a218cf8943f22 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -54,11 +54,6 @@ collect: 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)