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Fix malformed input to MEGAHIT with non-run-merged SEdata#558

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jfy133 merged 11 commits intodevfrom
fix-cat-se-data-dev
Jan 26, 2024
Merged

Fix malformed input to MEGAHIT with non-run-merged SEdata#558
jfy133 merged 11 commits intodevfrom
fix-cat-se-data-dev

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@jfy133 jfy133 commented Jan 16, 2024 •
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Closes #557

Also remove some extra dumps discovered during testing

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/mag 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).

@jfy133 jfy133 marked this pull request as draft January 16, 2024 05:47
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github-actions Bot commented Jan 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ff0c4aa

+| ✅ 161 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-19 13:46:19

@jfy133 jfy133 marked this pull request as ready for review January 16, 2024 08:22
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jfy133 commented Jan 16, 2024
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jfy133 commented Jan 19, 2024

@nf-core-bot fix linting

CarsonJM
CarsonJM approved these changes Jan 26, 2024
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LGTM!

@jfy133 jfy133 merged commit eb97cbd into dev Jan 26, 2024
@jfy133 jfy133 deleted the fix-cat-se-data-dev branch February 5, 2024 14:52
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@CarsonJM CarsonJM CarsonJM approved these changes

@maxibor maxibor Awaiting requested review from maxibor

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

@HadrienG HadrienG Awaiting requested review from HadrienG

@prototaxites prototaxites Awaiting requested review from prototaxites prototaxites is a code owner

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