[New module] Infernal cmsearch
Adds a module for infernal's cmsearch tool. Pretty much a drop-in replacement for hmmsearch - I've basically cloned the module in its entirety.
[DONE] Once https://github.com/nf-core/test-datasets/pull/1542 is in I'll change the path to the model file in the tests.
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Thanks for the review!
Because the tool is by the same authors of (and has the same interface as) hmmer/hmmsearch, I copied the module code itself almost verbatim from https://github.com/nf-core/modules/blob/master/modules/nf-core/hmmer/hmmsearch/main.nf.
I would tend to agree about leaving the optional flags to the args, but left it as-is to keep the same interface as the other module. Happy to drop it though, but in which case, do you think the module still try and gzip optional outputs if they exist? In large cases I imagine they could become quite sizable.
OK, have looked into removing these val inputs - having taken some input on the #modules Slack (https://nfcore.slack.com/archives/CJRH30T6V/p1742982305507179) - I think in this case they're better to leave in, as there is a lot of ambiguity in the possible file names a user could specify in ext.args that wouldn't match the output block specifications, especially for the .tbl output which is a commented tabular format. This way we can enforce a schema on file extensions, which also makes the gzip compression element more stable too.