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Commit e7937756 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Move parseMetadata unit ci if statements to single line

parent 1310010d
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2 merge requests!37v0.0.1,!28Resolve "Move inference to start of pipeline"
Pipeline #6638 failed with stages
in 5 minutes and 19 seconds
......@@ -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:
......
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