Bump openms version to 3.5.0 and migrate to version topics #9638
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we haven't gotten the anchor syntax to work properly yet, so for now you need to duplicate the entries. I reran everything with the most recent dev version of tools and |
should do the same thing...
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I hope it was okay, that i pushed some fixes directly to your PR. |
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Sure thing, thanks for fixing it @mashehu! |
modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap
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We have a proceedure for deprecating modules:
https://nf-co.re/docs/guidelines/components/module_deprecation
…st.snap Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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@nf-core-bot fix linting |
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Thanks for the hint @SPPearce! No matter what I do, I cannot get the linter to pass the cometadapter module. |
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I'll have another look. |
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I'm puzzled. I did the --fix option as well as tried out other things as well with nf-core 3.5.1 linter. I had the same solution afaik but locally I got the linting error. Anyways, looks like it works now, thanks! |
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there are some fixes in the dev version of tools (updated yesterday), that is also the version CI uses in modules (topics are still quite hot and we keep finding edge cases) |
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Alright, thanks again! Looks like we are ready to review here :) |
| output: | ||
| tuple val(meta), path("*.fasta"), emit: decoy_fasta | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions_openms, topic: versions |
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Oh this is really really long, I'm sure AI could make it much shorter.
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I tried already a full Gemini3 day on version parsing 😂😂
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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Can we merge? 😁 |
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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Is your local nf-core lint from 3.5.1? I guess the dev branch used during CI is the reason why it works for you and not during CI, correct? |
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The linting is complaining because the meta.yml hasn't been updated to match |
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(the singularity errors are unrelated, need to update branch to get rid of them) |
| - openms: | ||
| type: string | ||
| description: The tool name | ||
| - "FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\\$//' | sed 's/ -*//; s/ .*\\$//'": |
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| - "FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\\$//' | sed 's/ -*//; s/ .*\\$//'": | |
| - "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": |
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Linter seems to fail for topic channels currently. Tried to implement suggestion from Slack: https://nfcore.slack.com/archives/C09LJTQQ3EY/p1763134358185619?thread_ts=1762763322.812579&cid=C09LJTQQ3EY
Versions are captured properly in snapshot, though.
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda