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Commit ded8b61b authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add back ends manual to ci unit for parse, but manual

parent f83a3d8c
2 merge requests!65Develop,!64Resolve "samtools sort: couldn't allocate memory for bam_mem"
Pipeline #9057 canceled with stages
in 4 minutes and 43 seconds
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.gitlab-ci.yml
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View file @ ded8b61b
......@@ -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)
......
workflow/tests/test_parseMetadata.py
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View file @ ded8b61b
......@@ -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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