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Commit b36bb08e authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix path of script for unit test

parent 2ab086d2
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2 merge requests!37v0.0.1,!22Resolve "process_count"
Pipeline #6238 failed with stages
in 11 minutes and 28 seconds
......@@ -81,7 +81,7 @@ makeFeatureCounts:
stage: unit
script:
- singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
- pytest -m makeFeatureCounts
fastqc:
......
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