diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3dbb78e6e8ddcd4b22991484bae4bddd9bb32bdb..add0a9b8765623c74e59deadf180e2739c2a7da7 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -80,7 +80,7 @@ makeBigWig: 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` -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam + - 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` -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene_name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts - pytest -m makeFeatureCounts