From 656bd8b4a8cda80e5a4b096c4db6ee739f0253e6 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 09:29:51 -0600
Subject: [PATCH] Update inputs and outputs of make feature counts ci unit test
match new format
---
.gitlab-ci.yml | 4 ++--
workflow/tests/test_makeFeatureCounts.py | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bd9fea3..410aafb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -205,8 +205,8 @@ countData:
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://gudmaprbk/subread2.0.1:1.0.0' 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://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' 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://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
- singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
- assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
- singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index f6373b9..e147935 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -12,7 +12,7 @@ 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.countData'))
+ 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(
--
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