Claude/fix pr 82 q dwst#83
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- linting.yml: use && in non-release lint condition so only one of the two lint steps runs per PR, and gate PR_number.txt write on a present pull_request.number to avoid producing empty/invalid values. - linting_comment.yml: validate the PR number from the artifact and skip the comment step instead of hard-failing when the file is missing, empty, or malformed. - fix_linting.yml: skip the commit step when prek's failure left no staged changes so the workflow doesn't fail on an empty commit. - branch.yml: drop the duplicate "is" in the PR-target failure message. - .dockstore.yml: restore subclass casing to NFL (Dockstore is case-sensitive for Nextflow workflows). - AGENTS.md: update documented nf-schema version to 2.6.1 to match the pin in nextflow.config. https://claude.ai/code/session_01NegkDFUUqPkuCnE2YJ4oAU
Promote the Unreleased/2.1.0dev section to a dated 2.1.0 entry using the existing release-name convention (matches the 2.0.0 "Rome" entry). https://claude.ai/code/session_01NegkDFUUqPkuCnE2YJ4oAU
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ThermoRawFileParser already emits indexed mzML (-f=2 default) and the wiff converter does the same, so the OpenMS FileConverter pass is only useful for user-supplied pre-built mzML that may be unindexed. DIA-NN handles unindexed mzML on its own. Flip the default off; users who need it can opt in with --reindex_mzml true. Schema description and CHANGELOG updated to call out the migration note. https://claude.ai/code/session_01NegkDFUUqPkuCnE2YJ4oAU
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).