diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 888e01cd1df9c326dc1781560449736bf8d7e583..0835d45e564739f6108c2cdc937ce185221376d8 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 45cc33a8dde6d49a405d579306c720a39c3811f2..5a14fcd885b79d944e46de5d936d17fc941def7b 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