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Add module dragonflye for long-reads assembly #104

Merged
merged 13 commits into from
Nov 2, 2023
Merged

Add module dragonflye for long-reads assembly #104

merged 13 commits into from
Nov 2, 2023

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Daniel-VM
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@Daniel-VM Daniel-VM commented Oct 30, 2023 •
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PR description

The dragonflye pipeline has been added to nf-core/bacass to perform long-reads assembly.

Most relevant enhancements:

  • Added dragonflye module

  • Added a new test profile to test dragonflye performance (conf/test_long_dragonflye.config).

  • Introduced an intermediary step that detects assemblies needing additional processing (decompression) for gene annotation.

  • The GenomeSize field from the input samplesheet has been incorporated into the meta section of the ch_input + schema_input.json.

Closes #101

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 30, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit c3ad68a

+| ✅ 159 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-02 15:18:14

d4straub
d4straub approved these changes Nov 2, 2023
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LGTM, just some small comments.

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@Daniel-VM Daniel-VM merged commit 39de87c into nf-core:dev Nov 2, 2023
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@d4straub d4straub d4straub approved these changes

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