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Fix linting from a comment

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fix-linting.yml
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Add --help-json flag for machine-readable CLI help Fix linting from a comment #5370: Issue comment #4310 (comment) created by ewels
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Add --help-json flag for machine-readable CLI help Fix linting from a comment #5369: Issue comment #4310 (comment) created by ewels
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Add --help-json flag for machine-readable CLI help Fix linting from a comment #5368: Issue comment #4310 (comment) created by mashehu
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Add --help-json flag for machine-readable CLI help Fix linting from a comment #5367: Issue comment #4310 (comment) created by ewels
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nf-core modules info spaceranger/count results in a stack trace. Fix linting from a comment #5366: Issue comment #4309 (comment) created by mahesh-panchal
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Fix duplicate -b short flag in pipelines sync Fix linting from a comment #5365: Issue comment #4311 (comment) created by codecov Bot
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Add --help-json flag for machine-readable CLI help Fix linting from a comment #5364: Issue comment #4310 (comment) created by codecov Bot
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Fix dead link Fix linting from a comment #5363: Issue comment #4307 (comment) created by codecov Bot
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Update GitHub Actions Fix linting from a comment #5362: Issue comment #4306 (comment) created by codecov Bot
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Update GitHub Actions Fix linting from a comment #5361: Issue comment #4306 (comment) created by renovate Bot
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Convert params.genomes to a map structure instead of a nested parameters structure Fix linting from a comment #5360: Issue comment #4305 (comment) created by codecov Bot
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Update terminology from 'GitHub' to 'Git' Fix linting from a comment #5359: Issue comment #4304 (comment) created by codecov Bot
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nf-core modules container subcmd Fix linting from a comment #5358: Issue comment #4303 (comment) created by mashehu
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Fix nextflow info -d parsing in LocalWorkflow and preserve local_path path semantics Fix linting from a comment #5357: Issue comment #4302 (comment) created by codecov Bot
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fix(lint): use repo-root-relative path in git restore call in container_configs Fix linting from a comment #5356: Issue comment #4301 (comment) created by codecov Bot
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fix(lint): use repo-root-relative path in git restore call in container_configs Fix linting from a comment #5355: Issue comment #4301 (comment) created by codecov Bot
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fix(lint): use repo-root-relative path in git restore call in container_configs Fix linting from a comment #5354: Issue comment #4301 (comment) created by Copilot AI
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fix(lint): use repo-root-relative path in git restore call in container_configs Fix linting from a comment #5353: Issue comment #4301 (comment) created by jpfeuffer
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Fix edam comments Fix linting from a comment #5352: Issue comment #4242 (comment) created by LouisLeNezet
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Plugin to view .nextflow.log files using toolong Fix linting from a comment #5351: Issue comment #2895 (comment) created by ewels
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Add option to disable creating container configs Fix linting from a comment #5350: Issue comment #4295 (comment) created by mashehu
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Update pre-commit hooks Fix linting from a comment #5349: Issue comment #4298 (comment) created by codecov Bot
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Update GitHub Actions Fix linting from a comment #5348: Issue comment #4297 (comment) created by renovate Bot
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fix CI: commit updated configs after modules update step Fix linting from a comment #5347: Issue comment #4292 (comment) created by codecov Bot
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Fix linting for modules.json to add support for only installing subworkflows from a repository Fix linting from a comment #5346: Issue comment #4287 (comment) created by mashehu
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