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Commit 3c9c7d4d authored by Jonathan Gesell's avatar Jonathan Gesell
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Changed tag from 'gene_id' to 'gene_name'

parent 3f71105b
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2 merge requests!37v0.0.1,!22Resolve "process_count"
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workflow/rna-seq.nf
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......@@ -401,9 +401,9 @@ process makeFeatureCounts {
script:
"""
if [ "${endsManual_featureCounts }" == "se" ]; then
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
elif [ "${endsManual_featureCounts }" == "pe" ]; then
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
fi;
Rscript calculateTPM.R --count "${repRID}.featureCounts";
"""
......
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