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Commit a9b7c868 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Fix countData unit summary file name

parent 06983662
2 merge requests!37v0.0.1,!36Metadata output update
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This commit is part of merge request !36. Comments created here will be created in the context of that merge request.
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......@@ -107,7 +107,7 @@ countData:
script:
- singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
- assignedReads=$(grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)')
- assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
- pytest -m makeFeatureCounts
makeBigWig:
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