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Add SubWorkflow: mmseqs_contig_taxonomy #5524

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merged 16 commits into from May 21, 2024
Merged

Add SubWorkflow: mmseqs_contig_taxonomy #5524

merged 16 commits into from May 21, 2024

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Darcy220606
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@Darcy220606 Darcy220606 commented Apr 25, 2024 •
edited

PR checklist

Purpose: This PR adds a subworkflow that combines multiple mmseqs tools.
Function: This adds taxonomic classification to input 'nucleotide' sequences (e.g. contigs) , which can potentially be used in multiple pipelines, e.g. nf-core/funcscan and nf-core/taxprofiler.

  • 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

@Darcy220606 Darcy220606 requested a review from a team as a code owner April 25, 2024 08:38
@Darcy220606 Darcy220606 requested review from leoisl and removed request for a team April 25, 2024 08:38
Joon-Klaps
Joon-Klaps requested changes May 3, 2024
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Small changes, very nice contribution!

subworkflows/nf-core/mmseqs_contig_taxonomy/main.nf Outdated Show resolved Hide resolved
subworkflows/nf-core/mmseqs_contig_taxonomy/main.nf Outdated Show resolved Hide resolved
subworkflows/nf-core/mmseqs_contig_taxonomy/meta.yml Outdated Show resolved Hide resolved
subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test Show resolved Hide resolved
subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test Outdated Show resolved Hide resolved
Joon-Klaps
Joon-Klaps approved these changes May 17, 2024
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🚀

@Darcy220606 Darcy220606 added this pull request to the merge queue May 21, 2024
Merged via the queue into nf-core:master with commit f6ef5ce May 21, 2024
12 checks passed
@Darcy220606 Darcy220606 deleted the mmesqs_taxonomy_contigs branch May 21, 2024 07:45
tstoeriko pushed a commit to tstoeriko/nf-core-modules that referenced this pull request May 22, 2024
@Darcy220606 @tstoeriko
Add SubWorkflow: mmseqs_contig_taxonomy (nf-core#5524)
6814bd2 
* add mmseqs_contig_taxonomy

* apply prettier

* code linting

* changed the test dataset to bacteroides_fragilis instead of influenzae

* give more memory to mmseqs-taxa

* memory increased to 16.GB

* increase the process mem requirements

* fix memory

* add reviewer suggestion

* change back memory

* fix snap

* fix snap
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@Joon-Klaps Joon-Klaps Joon-Klaps approved these changes

@leoisl leoisl Awaiting requested review from leoisl leoisl is a code owner automatically assigned from nf-core/nf-test

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