diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 01eda4db944eb0c530130dbaf89c1adfab357b9d..33b100165d8ccac73a1b1bd6f6a82fc3da95bec9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -68,7 +68,7 @@ collect: 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& + 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=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2) @@ -84,7 +84,7 @@ collect: picardImg=$(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& + 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)