diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 659eadf19924560e144dd8fe67b08e999c287781..fb8278fc8178566f9e1d93ae91f9ed2270f3c269 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -39,7 +39,6 @@ parseMetadata: - spike=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike) - species=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species) - readLength=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.stageNew.csv" -p readLength) - - readLength=""${readLength} echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv - pytest -m parseMetadata diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 9b77129a3b66f325d61c3bf87ba3a0466ef90da0..1443869ba42180f4ec83b52fb4cf15c078e1c7a5 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -239,7 +239,6 @@ process parseMetadata { # get read length metadata readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p readLength) - readLength=""\${readLength} echo -e "LOG: read length metadata parsed: \${readLength}" >> ${repRID}.parseMetadata.log # gave design file diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py index 6257aec1e6d8f99528fafca091f7b6d5286f277a..500054264f7c8c50310da92d9995f432930318d3 100644 --- a/workflow/scripts/parseMeta.py +++ b/workflow/scripts/parseMeta.py @@ -105,7 +105,7 @@ def main(): # Get read length metadata from 'Experiment Settings.csv' if (args.parameter == "readLength"): readLength = metaFile.Read_Length.unique() - print(str(readLength)) + print(str(readLength).strip('[]')) if __name__ == '__main__': main()