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Add new module called rundbcan and subcommands(database, cazymeannotation, easycgc, easysubstrate) #8216

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@Xinpeng021001 Xinpeng021001 commented Apr 4, 2025

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
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  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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    • For subworkflows:
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@Xinpeng021001 Xinpeng021001 reopened this Apr 4, 2025
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SPPearce commented Apr 7, 2025

I will say in future can you please make individual PRs for subtools, it will be easier and faster for you to get them reviewed one at a time than all together.

@Xinpeng021001
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I will say in future can you please make individual PRs for subtools, it will be easier and faster for you to get them reviewed one at a time than all together.

I'm really sorry for the inconvenience. I'll split the tools next time.

Comment on lines +9 to +11
tuple val(meta), path(input_raw_data)
tuple val(meta), path(input_gff)
tuple val(meta), val (gff_type)
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Same as above, I think the gff_type could be with the gff itself, and you can't have meta multiple times.

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Could each of the tools (except the database generation) create the files directly in the work directory, instead of inside a folder? You would then want to rename them with the prefix after creation, because it looks like it makes the files with identical filenames, but it'll mean that the output folders wouldn't be nested in the same way.

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Could each of the tools (except the database generation) create the files directly in the work directory, instead of inside a folder? You would then want to rename them with the prefix after creation, because it looks like it makes the files with identical filenames, but it'll mean that the output folders wouldn't be nested in the same way.

I'm sorry, but the run_dbcan tool won't give the output files individually; the entire output folder contains all outputs. This is an original design from a previous developer, and I kept the same idea from them.

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