diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 8df331b6f4ebe20f6f880bfcd948c7a48986b94d..8dd2e7a245def0ef28681d04b852cf88e23a977b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -162,7 +162,6 @@ seqwho: - version_seqwho.txt expire_in: 7 days - trimData: stage: unit only: @@ -197,30 +196,30 @@ downsampleData: - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq - pytest -m downsampleData - inferMetadata: - stage: unit - only: - - push - - tags - except: - - merge_requests - - schedules - script: - - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt - - > - align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) && - if [[ ${align} == "" ]]; then exit 1; fi - - > - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log && - ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` && - if [[ ${ended} == "" ]]; then exit 1; fi - - pytest -m inferMetadata - artifacts: - name: "$CI_JOB_NAME" - when: always - paths: - - version_rseqc.txt - expire_in: 7 days +inferMetadata: + stage: unit + only: + - push + - tags + except: + - merge_requests + - schedules + script: + - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt + - > + align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) && + if [[ ${align} == "" ]]; then exit 1; fi + - > + singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log && + ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` && + if [[ ${ended} == "" ]]; then exit 1; fi + - pytest -m inferMetadata + artifacts: + name: "$CI_JOB_NAME" + when: always + paths: + - version_rseqc.txt + expire_in: 7 days alignData: stage: unit