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Allow input pattern validation for csv/tsv/txt #118

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ojziff opened this issue Oct 18, 2022 · 3 comments
Closed

Allow input pattern validation for csv/tsv/txt #118

ojziff opened this issue Oct 18, 2022 · 3 comments
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enhancement Improvement for existing functionality
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@ojziff
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ojziff commented Oct 18, 2022

Description of the bug

minor point, but why does --input have to match pattern ^\S+.txt$ Since the input is just a single column of SRR identifiers, it could be csv or tsv.

Command used and terminal output

nextflow run nf-core/fetchngs \
--input srr_id.txt \
--outdir reads \
--force_sratools_download -profile crick -r 1.7 -resume

Referring to:
see

"pattern": "^\\S+\\.txt$",
and
"pattern": "^\\S+\\.txt$",

@ojziff ojziff added the bug Something isn't working label Oct 18, 2022
@Midnighter Midnighter added enhancement Improvement for existing functionality and removed bug Something isn't working labels Oct 19, 2022
@Midnighter
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I don't see a good reason. Was there one that I forgot about @drpatelh ?

@drpatelh
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drpatelh commented Nov 2, 2022

Somewhat a duplicate of #111

@drpatelh drpatelh added this to the 1.8 milestone Nov 4, 2022
@drpatelh drpatelh closed this as completed Nov 4, 2022
@drpatelh
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drpatelh commented Nov 4, 2022

Fixed in d67b3ef

@drpatelh drpatelh changed the title why does input file need to end in .txt Allow input pattern validation for csv/tsv/txt Nov 4, 2022
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