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add module for pbptyper#2005

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rpetit3 merged 5 commits into
nf-core:masterfrom
rpetit3:rp3-add-pbptyper
Sep 7, 2022
Merged

add module for pbptyper#2005
rpetit3 merged 5 commits into
nf-core:masterfrom
rpetit3:rp3-add-pbptyper

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@rpetit3 rpetit3 commented Sep 2, 2022 •
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PR checklist

Closes #2004

  • 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 the new module Adding a new module label Sep 2, 2022
@rpetit3 rpetit3 self-assigned this Sep 2, 2022
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rpetit3 commented Sep 2, 2022

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The singularity container isn't available yet, will keep an eye on it and retry in a few days

jfy133
jfy133 requested changes Sep 7, 2022
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Missing optional input parameter of --db but otherwise LGTM!

@rpetit3

rpetit3 commented Sep 7, 2022

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Thank you!

@rpetit3 rpetit3 merged commit a5976c5 into nf-core:master Sep 7, 2022
@rpetit3 rpetit3 deleted the rp3-add-pbptyper branch September 7, 2022 21:29
matthdsm pushed a commit to matthdsm/nf-core-modules that referenced this pull request Sep 28, 2022
@rpetit3 @matthdsm
add module for pbptyper (nf-core#2005)
a18f931 
* add module for pbptyper

* add optional database parameter
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@jfy133 jfy133 jfy133 approved these changes

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new module: pbptyper

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