diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3491d360a870c1a31511d6d856c3a8e7684e8cb3..ad7330b0562bf507ca43b0d4c0d457e2b8cc1d12 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -121,8 +121,7 @@ dataQC: stage: unit script: - echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls - - for i in {"chr8","chr4","chrY"}; do - echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls + - pytest -m dataQC