diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index acb9bec55c2d4298b979c6db9a96e9a50b134928..907fd30bbbb7599881ff8813deb31bda83247bbf 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -40,17 +40,11 @@ inferMetadata: script: - > align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5JA_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) - if [[ ${align} == "" ]] - then - exit 1 - fi + if [[ ${align} == "" ]]; then exit 1; fi - > singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam" 1>> Q-Y5JA_1M.se.inferMetadata.log ended=`singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5JA_1M.se.inferMetadata.log` - if [[ ${ended} == "" ]] - then - exit 1 - fi + if [[ ${ended} == "" ]]; then exit 1; fi - pytest -m inferMetadata getRef: