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Added MetaPlAn subworkflow #5356

Merged
merged 17 commits into from
Mar 25, 2024
Merged

Added MetaPlAn subworkflow #5356

merged 17 commits into from
Mar 25, 2024

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LaurenGonsalves
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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.
  • 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

@LaurenGonsalves LaurenGonsalves requested review from vagkaratzas and removed request for a team March 20, 2024 21:19
@LaurenGonsalves LaurenGonsalves self-assigned this Mar 20, 2024
@LaurenGonsalves LaurenGonsalves linked an issue Mar 20, 2024 that may be closed by this pull request
new subworkflow: FASTQ/TAXONOMIC_PROFILE/METAPHLAN #5294
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@CarsonJM CarsonJM self-requested a review March 20, 2024 22:45
CarsonJM
CarsonJM requested changes Mar 20, 2024
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@CarsonJM CarsonJM left a comment

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Nice! Great work! Just a few changes

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf Outdated Show resolved Hide resolved
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subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf Outdated Show resolved Hide resolved
subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf Outdated Show resolved Hide resolved
subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/meta.yml Show resolved Hide resolved
subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/tests/main.nf.test Outdated Show resolved Hide resolved
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subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/tests/nextflow.config Outdated Show resolved Hide resolved
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maxulysse
maxulysse approved these changes Mar 21, 2024
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Minor suggestions

@maxulysse
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I can see that all_samples.txt doesn't have a common md5 between conda and docker, can you check the content?
I'm assuming that some specific lines would be specific to conda, so either a path to the lib, in which case, I'd suggest snapshotting some of this file's lines, or maybe a different version of a dependency, in which case, I'd add this as a dependency in the environment.yml, similarly to what we've done already with samtools

@CarsonJM CarsonJM disabled auto-merge March 25, 2024 22:50
@CarsonJM CarsonJM enabled auto-merge March 25, 2024 22:50
@CarsonJM CarsonJM added this pull request to the merge queue Mar 25, 2024
Merged via the queue into nf-core:master with commit 4328ba3 Mar 25, 2024
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jvfe added a commit that referenced this pull request Mar 26, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
b4ee797 
* master: (47 commits)
  Update genomescope2 module and add nf-tests (#5399)
  PLINK/GWAS additional output (#5387)
  Plink linkage disequilibrium additional output (#5388)
  new module: Plink epistasis analysis  (#5386)
  Add module for TaxonKit name2taxid (#4778)
  Update-cellranger-modules (#5016)
  Update: GTDBTK/CLASSIFYWF (migrate to nf-test and only execute mv when dirs actually present) (#5390)
  Added MetaPlAn subworkflow (#5356)
  port `vcftools` to nf-test (#5375)
  Update modules: rgi (#5383)
  Update condaforge/mambaforge Docker tag to v24 (#5381)
  Update gecco + migrate to nf-test (#5372)
  Update learnmsa module to work with compressed files. (#5276)
  New module: kraken2/build  (#5212)
  Update kalign module to work with compressed files. (#5277)
  port `ensemblvep/download` to nf-test (#5373)
  port `manta-germline` to nf-test (#5362)
  port `tiddit-sv` to nf-test and add `--threads` (#5371)
  Decoupler module (#5317)
  fix optional cram support in modules and migrate to nf-test (#5329)
  ...
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@CarsonJM CarsonJM CarsonJM approved these changes

@maxulysse maxulysse maxulysse approved these changes

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee

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

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new subworkflow: FASTQ/TAXONOMIC_PROFILE/METAPHLAN
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@LaurenGonsalves @maxulysse @CarsonJM