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Fix missing concoct globs #514

Merged
merged 4 commits into from
Sep 27, 2023
Merged

Fix missing concoct globs #514

merged 4 commits into from
Sep 27, 2023

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jfy133
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@jfy133 jfy133 commented Sep 26, 2023 •
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Wait until #511 is merged! Then test before requesting review!

closes #510 to ensure we always pick up CONCOCT related files after CONOCT itself

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 Sep 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3943efa

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ 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

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-27 11:20:19

jfy133
jfy133 commented Sep 26, 2023
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@jfy133 jfy133 requested a review from maxibor September 26, 2023 17:25
@jfy133 jfy133 changed the title [DO NOT MERGE] Fix missing concoct globs Fix missing concoct globs Sep 27, 2023
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jfy133 commented Sep 27, 2023

testing...

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jfy133 commented Sep 27, 2023

@maxibor I've tested this and it should work except DASTool does not find any bins from the CONCOCT bins with the current test data... do you have anything you can double check?

d4straub
d4straub approved these changes Sep 27, 2023
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LGTM

prototaxites
prototaxites approved these changes Sep 27, 2023
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LGTM also!

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jfy133 commented Sep 27, 2023

It should be a simple enough change so I will merge, and hopefully test with an updated full test (PR coming soon, once I've finished downloading the massive file from Australia and uploaded ti iGenomes...) 👍

@jfy133 jfy133 merged commit 3cd0541 into dev Sep 27, 2023
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@jfy133 jfy133 deleted the fix-missing-concoct-globs branch September 27, 2023 14:47
jfy133 added a commit that referenced this pull request Sep 27, 2023
@jfy133
Merge pull request #515 from nf-core/fix-gunc-overwriting
e8316ab 
Fix missing GUNC overwriting #514
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
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@prototaxites prototaxites prototaxites approved these changes

@d4straub d4straub d4straub approved these changes

@maxibor maxibor Awaiting requested review from maxibor

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@jfy133 @prototaxites @d4straub