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@rpetit3 rpetit3 commented Sep 29, 2021

PR checklist

Closes #766

  • 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
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

This PR adds a module for mashtree. Mashtree allows different inputs (FASTA, FASTQ, Genbank, Mash sketches) so I just called them seqs. If there is a better variable name please let me know.

Test outputs

test.dnd

(genome:0.18629,test_1:0.18629);

test.tsv

.       genome  test_1
genome  0       0.372583
test_1  0.372583        0

versions.yml

MASHTREE:
    mashtree: 1.2.0

@rpetit3 rpetit3 mentioned this pull request Sep 29, 2021
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@rpetit3 rpetit3 added Ready for Review new module Adding a new module and removed Ready for Review labels Sep 29, 2021
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@drpatelh drpatelh left a comment

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👌🏽

@drpatelh drpatelh merged commit 7d98bf1 into nf-core:master Oct 5, 2021
@rpetit3 rpetit3 deleted the rp3-add-mashtree branch October 5, 2021 20:36
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new module: mashtree

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