Update unit test for count #73

.gitlab-ci.yml

@@ -105,6 +105,8 @@ dedupData:
 countData:
   stage: unit
   script:
+  - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
+  - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
   - 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' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -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.countData
   - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se