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Fix bug in assembly input code#445

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prototaxites merged 4 commits intonf-core:devfrom
prototaxites:fix_assembly_input
May 17, 2023
Merged

Fix bug in assembly input code#445
prototaxites merged 4 commits intonf-core:devfrom
prototaxites:fix_assembly_input

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@prototaxites prototaxites commented May 17, 2023 •
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Realised right after merging that there was a pretty catastrophic bug in the assembly input code 🤦‍♂️ I thought I had figured out the distinction between meta.id and meta.group for the input, but there were filename collisions for a couple of combinations of --binning_map_mode and --coasssemble_group which I had missed...

Fix separates the id and group columns for the assembly input CSV, which should ensure collisions cannot happen, and updated docs accordingly.

Also adds test_binning_entry to nextflow.config, which I had forgotten to do...

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).

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github-actions Bot commented May 17, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @prototaxites,

It looks like this pull-request is has been made against the prototaxites/mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the prototaxites/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@prototaxites prototaxites changed the base branch from master to dev May 17, 2023 12:56
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github-actions Bot commented May 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e69a979

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-17 15:44:43

jfy133
jfy133 approved these changes May 17, 2023
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Makes sense to me

Comment thread CHANGELOG.md
@prototaxites prototaxites merged commit 97a7b31 into nf-core:dev May 17, 2023
@prototaxites prototaxites deleted the fix_assembly_input branch May 17, 2023 18:01
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