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add module for pasty #2003

Merged
merged 6 commits into from
Sep 7, 2022
Merged

add module for pasty #2003

merged 6 commits into from
Sep 7, 2022

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rpetit3
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@rpetit3 rpetit3 commented Sep 2, 2022 •
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PR checklist

Closes #2002

  • 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

Docker and Singularity are in the works: BioContainers/containers#467

@rpetit3 rpetit3 added the new module Adding a new module label Sep 2, 2022
@rpetit3 rpetit3 self-assigned this Sep 2, 2022
FriederikeHanssen
FriederikeHanssen reviewed Sep 7, 2022
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modules/pasty/main.nf
pasty \\
$args \\
--prefix $prefix \\
--assembly $fasta
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can't use any additional threads? In that case, would it be suitable to switch to process_single ?

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good catch!

@rpetit3
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rpetit3 commented Sep 7, 2022

Thank you!

@rpetit3 rpetit3 merged commit 3ef618f into nf-core:master Sep 7, 2022
@rpetit3 rpetit3 deleted the rp3-add-pasty branch September 7, 2022 15:29
matthdsm pushed a commit to matthdsm/nf-core-modules that referenced this pull request Sep 28, 2022
@rpetit3 @matthdsm
add module for pasty (nf-core#2003)
a02c6e1 
* add module for pasty

* run prettier

* line up those commas

* Update main.nf
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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new module: pasty
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@rpetit3 @FriederikeHanssen