Pass a list of modules/subworkflows(files) to nf-core modules lint #3140
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* ci: Attempt to split everything out Don't hate me Adam * ci: Add changed since, sharding, and ci * ci: Add filter to try to get jobs split up * ci: Switch to only-changed * ci: See if follow-dependencies works without "related-tests" * ci: Remove skipped tests Idk what we're going to do about these... * ci: Actually use the nf-test version * ci: module => process * ci: Clean up job names * dummy: Make a change * ci: Skip test.tap * ci: Add fetch-depth * ci: Clean up name * ci: Lint everything * ci: Get the job names clean * ci: Add hide-progress on linting * ci: Add psuedocode for conda-fail.yml https://nfcore.slack.com/archives/CJRH30T6V/p1724406283145319 * test: Snapshot the versions contents, not the hash #6505 * ci: Keep running nf-core lint the way it was Blocked by nf-core/tools#3140 * ci: Move conda skips out * ci: Address a comment * style: Move prettier and editorconfig to pre-commit #4554 (comment) * ci: Add note about nf-core lint pre-commit * chore: Copy over conda skips a004c86 2da71b7 * ci: only-changed => changed-since * Add confirm-pass * ci: dynamically set shards * ci: Run 3 process jobs per CI run as an example * install nf-test * fix install nf-test * fix install nf-test * ci: Remove dynamic number of shards, and combine process and workflow filters * ci: Remove variable Nextflow versions * test: Update bowtie versions * ci: Fix indention * ci: We're not testing multiple python versions * style: Clean up job names * build: Remove invisible characters? * test(bowtie): Bump snapshots * style: Remove stray comment * ci: Add GPU tests in their own workflows These will only get trigger on the paths listed * ci(gpu): Clean up triggers and make a note about how to make the includes smarter * ci: pip install cryptography * ci: Try removing path * ci: Add fetch-depth and remove duplicate checkout * test: Remove the second gpu profile * ci: Add path back in * ci(gpu): Remove changed-since * ci: Fix missed dorny/paths-filter update Co-authored-by: mashehu <mashehu@users.noreply.github.com> * Add changes from codereview Co-authored-by: mashehu <mashehu@users.noreply.github.com> * style: Remove example TODO comments https://github.com/nf-core/modules/pull/6286/files#r1846856369 Co-authored-by: mashehu <mashehu@users.noreply.github.com> * refactor: Try tags for GPU CI askimed/nf-test#272 * style: Set NFT_WORKDIR as an ENV variable * style: Run lsp format on a parabricks module For science * test: Add gpu tags to parabricks * ci: Split tags out of matrix * Revert "style: Run lsp format on a parabricks module" This reverts commit d134e78. * ci: Fix name --------- Co-authored-by: Edmund Miller <emiller@jodie.attlocal.net> Co-authored-by: maxulysse <max.u.garcia@gmail.com> Co-authored-by: mashehu <mashehu@users.noreply.github.com>
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Description of feature
I was working on nf-core/modules#6286 last week.
I really wanted to avoid using path-filter and having the whole separate step logic for the linting.
I think we could offload the changed files to pre-commit, and create pre-commit hooks for nf-core/tools. I think it would be pretty slick for pipelines as well(I know I don't run nf-core lint often enough personally)
The only issue I had was the way pre-commit passes files. It will pass
nf-core modules lint modules/nf-core/bowtie/align/main.nf modules/nf-core/bowtie/build/main.nf modules/nf-core/fastqc/main.nf ...which currently doesn't work.The text was updated successfully, but these errors were encountered: