Hello friends, We found that many nf-core subworkflows have inconsistencies in inputs/outputs between the

<http://main.nf|main.nf>

and

meta.yml

. This came up because we are building the auto-import of nf-core subworkflows into the Nextflow registry and we want to make sure the module specs are correct PR: github.com/nf-core/modules/pull/12882 It is ready from my end but I understand that modules are typically updated one at a time. Let me know how you want to handle these fixes. I can split into ~100 PRs if you want 😅 cc @Jonathan Manning

Please no to the 100+ PRs. Let's merge it in a block.

I think the bigger question from our side is how did this get past linting? The linting should check these are consistent

The subworkflows haven't been linting properly (or at all?)

ah, true

The modules ones are mostly just reordering

yeah I wasn't sure whether to include the process output reordering. I think my agent did that to make it "consistent" with the source code but it doesn't really matter. I can revert that part if you want

split it into two PR's I think

the reordering is fine

Thanks Simon!

No problem, thanks for doing the hard work, I just try and get things merged 😉