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Remove dodgy sniffer code from samplesheet_check.py #2194

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Merged
jfy133 merged 3 commits into from
Feb 27, 2023
Merged

Remove dodgy sniffer code from samplesheet_check.py #2194

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6c0bcf5
Remove problematic sniffer code resulting in no header found even whe…
jfy133 Feb 24, 2023
c6e9878
Update CHANGELOG.md
jfy133 Feb 24, 2023
6de786c
Update CHANGELOG.md
jfy133 Feb 24, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]

### Linting

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3 changes: 0 additions & 3 deletions nf_core/pipeline-template/bin/check_samplesheet.py
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Expand Up @@ -158,9 +158,6 @@ def sniff_format(handle):
peek = read_head(handle)
handle.seek(0)
sniffer = csv.Sniffer()
if not sniffer.has_header(peek):
logger.critical("The given sample sheet does not appear to contain a header.")
sys.exit(1)
dialect = sniffer.sniff(peek)
return dialect

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