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Add module muse/call #5630

Merged
merged 14 commits into from
Nov 29, 2024
Merged

Add module muse/call #5630

merged 14 commits into from
Nov 29, 2024
+269 −0

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famosab
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@famosab famosab commented May 17, 2024 •
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PR checklist

Closes #5621

  • 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.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • 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:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

The Docker image still needs to be pushed to the nf-core registry, then I can update the paths accordingly. Also relates to #5629

@famosab famosab requested a review from a team as a code owner May 17, 2024 14:18
@famosab famosab requested review from koenbossers and removed request for a team May 17, 2024 14:18
@SPPearce
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Could this tool be added to BioConda? Then the other containers would be generated automatically

@famosab
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famosab commented May 21, 2024

I opened a PR: bioconda/bioconda-recipes#47957

If that works, I will change the files in this PR accordingly

@famosab famosab requested a review from a team as a code owner November 15, 2024 09:34
@famosab famosab changed the title Add module muse/call and Dockerfile Add module muse/call Nov 15, 2024
SPPearce
SPPearce reviewed Nov 15, 2024
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A few comments.

modules/nf-core/muse/call/main.nf Outdated Show resolved Hide resolved
modules/nf-core/muse/call/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/muse/call/meta.yml Show resolved Hide resolved
modules/nf-core/muse/call/meta.yml Outdated Show resolved Hide resolved
SPPearce
SPPearce approved these changes Nov 16, 2024
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It would be good to check about the indexes (bam and fasta), but otherwise I'm happy.

modules/nf-core/muse/call/meta.yml Show resolved Hide resolved
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famosab commented Nov 18, 2024

I asked here: wwylab/MuSE#31
Will wait for their reply and merge afterwards :)

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famosab commented Nov 29, 2024

@SPPearce I added the .bai files alongside the .bam building ontop of the answer I got from the developers. Do you think its ok like this?

@famosab famosab requested a review from SPPearce November 29, 2024 13:19
SPPearce
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Ok, looks good to me now.

@famosab famosab enabled auto-merge November 29, 2024 13:57
@famosab famosab added this pull request to the merge queue Nov 29, 2024
Merged via the queue into nf-core:master with commit 219299d Nov 29, 2024
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@famosab famosab deleted the muse-call branch November 29, 2024 14:05
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@famosab
Add module muse/call (nf-core#5630)
98c3900 
* start work on muse/call

* correct command and add snap

* prettier

* exclude conda

* change to bioconda

* update snap

* add conda test

* update meta

* change process label

* add indices and update meta

* update containers and version extraction
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@SPPearce SPPearce SPPearce approved these changes

@koenbossers koenbossers Awaiting requested review from koenbossers koenbossers was automatically assigned from nf-core/nf-test

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new module: MuSE
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@famosab @SPPearce