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remove leading and trailing whitespaces from given target list #80

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alexg9010 opened this issue Dec 15, 2020 · 2 comments
Open

remove leading and trailing whitespaces from given target list #80

alexg9010 opened this issue Dec 15, 2020 · 2 comments
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sanity_check sanity checks for robust execution - abort early with meaningful messages

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@alexg9010
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alexg9010 commented Dec 15, 2020

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
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alexg9010 commented Dec 15, 2020

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
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#56

@borauyar borauyar added the sanity_check sanity checks for robust execution - abort early with meaningful messages label Mar 30, 2022
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