From 6e4ad75286c923e79a3c469d0cad9eb76f137656 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Mon, 24 Aug 2020 20:04:46 -0500 Subject: [PATCH] Update unit test for count #73 --- .gitlab-ci.yml | 3 ++- workflow/tests/test_makeFeatureCounts.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d0d3b39..a2477d4 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -106,7 +106,8 @@ countData: stage: unit 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' --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.featureCounts + - 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 - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)') - pytest -m makeFeatureCounts diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py index d741a2f..d33527a 100644 --- a/workflow/tests/test_makeFeatureCounts.py +++ b/workflow/tests/test_makeFeatureCounts.py @@ -11,5 +11,6 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.makeFeatureCounts def test_makeFeatureCounts(): - assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.featureCounts')) + assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.countData')) assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.countTable.csv')) + assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.tpmTable.csv')) -- GitLab