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Commit 8ce8b56e authored by Jonathan Gesell's avatar Jonathan Gesell
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Updated inferMetadata testing script

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3 merge requests!37v0.0.1,!27Develop,!26Resolve "Chunk bam for parallel tin calculation"
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......@@ -89,7 +89,8 @@ fastqc:
inferMetadata:
stage: unit
script:
- singularity run 'docker://bicf/rseqc3.0:2.0.0' tin.py -i ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed
- for i in {"chrNC_000001.11","chrNC_000002.12","chrNC_000019.10"}; do
echo " tin.py -i tin.py -i /test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5JA_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\"" | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j `nproc` -k > Q-Y5JA_1M.se.sorted.deduped.tin.xls
- pytest -m inferMetadata
integration_se:
......
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