From 8f5efffa3cf8ba1b602fe23f941b7a98f2ded0c1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 01:06:26 -0600
Subject: [PATCH] Remove ends manual from parse metadata unit ci
---
.gitlab-ci.yml | 3 +--
workflow/tests/test_parseMetadata.py | 2 +-
2 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f9a5b7b..d7fcaf6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -109,12 +109,11 @@ 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=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual)
- stranded=$(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)
- readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
- - echo -e "${endsMeta},${endsRaw},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
+ - echo -e "${endsMeta},${endsRaw},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
- pytest -m parseMetadata
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
index 5a14fcd..45cc33a 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,se,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
+ if line.strip() == "uk,uk,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
data = True
return data
--
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