From ded8b61ba14b8cd7caf3080050a72d0ac27861e8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 01:21:00 -0600
Subject: [PATCH] Add back ends manual to ci unit for parse, but manual
---
.gitlab-ci.yml | 1 +
workflow/tests/test_parseMetadata.py | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 888e01c..0835d45 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -109,6 +109,7 @@ parseMetadata:
- study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
- endsRaw=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
- endsMeta="uk"
+ - endsManual="se"
- stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
- spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
- species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
index 45cc33a..5a14fcd 100644
--- a/workflow/tests/test_parseMetadata.py
+++ b/workflow/tests/test_parseMetadata.py
@@ -19,7 +19,7 @@ def readLine(fileName):
data = False
file = open(fileName, "r")
line = file.readline()
- if line.strip() == "uk,uk,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
+ if line.strip() == "uk,uk,se,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
data = True
return data
--
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