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feat: allow adna co-binning #602

Merged
merged 3 commits into from
Apr 19, 2024
Merged

feat: allow adna co-binning #602

merged 3 commits into from
Apr 19, 2024

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maxibor
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@maxibor maxibor commented Mar 13, 2024 •
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This PR enables the possibility to perform co-binning when using the ancient DNA mode.

Once merged, it can close #572

PR checklist

  • This comment contains a description of changes (with reason).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@maxibor maxibor linked an issue Mar 13, 2024 that may be closed by this pull request
Please make --binning_map_mode group and --ancient-dna compatible features #572
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github-actions bot commented Mar 13, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 2f62ecd

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowMag.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-18 09:45:35

@maxibor maxibor requested review from jfy133 and d4straub March 13, 2024 15:26
jfy133
jfy133 approved these changes Apr 18, 2024
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Looks simple enough to me, if you're sure pydamage handles such BAM files in such a form (but I'm assuming you are ;) )

jfy133
jfy133 reviewed Apr 18, 2024
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CHANGELOG.md Outdated Show resolved Hide resolved
@jfy133 jfy133 merged commit a857f51 into nf-core:dev Apr 19, 2024
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@jfy133 jfy133 jfy133 approved these changes

@d4straub d4straub Awaiting requested review from d4straub

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Successfully merging this pull request may close these issues.

Please make --binning_map_mode group and --ancient-dna compatible features
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@maxibor @jfy133