From 6c0bcf59f00e9fbdb56108c51d3268a1ed6fbbda Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 24 Feb 2023 20:27:46 +0100 Subject: [PATCH 1/3] Remove problematic sniffer code resulting in no header found even when it exists See https://github.com/nf-core/funcscan/pull/227 --- nf_core/pipeline-template/bin/check_samplesheet.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py index 11b155723..4a758fe00 100755 --- a/nf_core/pipeline-template/bin/check_samplesheet.py +++ b/nf_core/pipeline-template/bin/check_samplesheet.py @@ -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 From c6e9878809fe7ab4abf72f0dbfee0734707904e1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 24 Feb 2023 20:31:28 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 67e6ada89..b9fe88e98 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 @jfy133] ### Linting From 6de786c53cf1d7c751de9c109cad6e76e101fd84 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 24 Feb 2023 20:31:41 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b9fe88e98..2f7204d37 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +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 @jfy133] +- 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