BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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remove leading and trailing whitespaces from given target list #80

Open alexg9010 opened 3 years ago

alexg9010 commented 3 years ago

When specifying multiple targets and some of the values have an additional space, the pipeline call fails

pigx-rnaseq -s tests/settings.yaml tests/sample_sheet.csv \
--target={deseq_report_salmon_transcripts, deseq_report_salmon_genes} \
--force -n
usage: pigx-rnaseq [-h] [-v] (--init [{settings,sample-sheet,both}] | -s SETTINGS) [-c CONFIGFILE] [--target TARGET] [-n] [--graph GRAPH] [--force] [--reason] [--unlock] [sample_sheet]
pigx-rnaseq: error: unrecognized arguments: deseq_report_salmon_genes}
alexg9010 commented 3 years ago

works without problems when space is removed:

pigx-rnaseq -s tests/settings.yaml tests/sample_sheet.csv \
--target=deseq_report_salmon_transcripts,deseq_report_salmon_genes} \
--force -n
borauyar commented 2 years ago

56