Important! Template update for nf-core/tools v4.0.2 (fixing conflicts)#60
Important! Template update for nf-core/tools v4.0.2 (fixing conflicts)#60vinisalazar wants to merge 18 commits into
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Keep current HEAD changes throughout; combine where incoming only adds (latest-everything NXF_VER in nf-test.yml, stable_path/stable_content variables in default.nf.test, multiqc/multiqc_logo/outdir take params in funcprofiler.nf). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- humann/humann4: rename duplicate `meta` input to `_meta` - profile: rename rgi_inputs to ch_input_for_rgi, add ch_input_for_eggnogmapper, fix shadowed `reads`/`profile` closure params to use underscore prefix - funcprofiler.nf: remove top-level statements (redundant, samplesheet/databases passed as workflow inputs) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Hi @vinisalazar thanks for working on this! Is there a reason this is a separate PR from #56? I'm not sure what changed. I don't know enough about the templating to do a good job reviewing these changes or know why the tests are failing; could you maybe ping the slack group for a reviewer? |
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@nickp60 that PR has many merge conflicts, this is an attempt to fix the conflicts. But, I think we may need to hold it off until v1.0.0 is merged. |
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@nickp60 I believe stuff's breaking because of version updates to the CI toolchain (especially nf-test). I guess the move here is merge v1.0.0 and then can look into that |
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Applying fixes after running 'nf-core modules lint' command
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- Remove action files while migration to v4 is not stable
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@nickp60 I did some work on this today and realised that it will need to be merged before v1.0.0, due to the fact that the CI checks on the v1.0.0 are checking against this version of the template |
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Supersedes #56
FIxing conflicts from the template update.
I used Claude to do most of the fixes and approved each one individually, but would be good to have more reviews.