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add module for mykrobe predict and genotyphi parse#1818

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SPPearce merged 4 commits into
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rpetit3:rp3-add-mykrobe-genotyphi
Sep 26, 2022
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add module for mykrobe predict and genotyphi parse#1818
SPPearce merged 4 commits into
nf-core:masterfrom
rpetit3:rp3-add-mykrobe-genotyphi

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@rpetit3 rpetit3 commented Jun 28, 2022

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PR checklist

Closes #1817

  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@rpetit3 rpetit3 added new module Adding a new module Ready for Review labels Jun 28, 2022
sguizard
sguizard reviewed Jul 4, 2022
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Comment thread modules/mykrobe/predict/main.nf
sguizard
sguizard approved these changes Jul 6, 2022
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LGTM

@SPPearce SPPearce merged commit 6d6e3a0 into nf-core:master Sep 26, 2022
matthdsm pushed a commit to matthdsm/nf-core-modules that referenced this pull request Sep 28, 2022
@rpetit3 @SPPearce @matthdsm
add module for mykrobe predict and genotyphi parse (nf-core#1818)
300b337 
* add module for mykrobe predict and genotyphi parse

* Update meta.yml

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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new module: Mykrobe and GenoTyphi

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@rpetit3 @sguizard @SPPearce