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Fix missing GUNC overwriting #514 #515

Merged
merged 6 commits into from
Sep 27, 2023
Merged

Fix missing GUNC overwriting #514 #515

merged 6 commits into from
Sep 27, 2023

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jfy133
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@jfy133 jfy133 commented Sep 26, 2023

Wait until #511 is merged! Then test before requesting review!

closes #502 to stop GUNC overwriting otuput directories when running with domain classification

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 f9691cf

+| ✅ 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 14:50:14

@jfy133 jfy133 requested a review from maxibor September 26, 2023 17:25
@jfy133 jfy133 changed the title [DO NOT MERGE] Fix missing GUNC overwriting #514 Fix missing GUNC overwriting #514 Sep 27, 2023
jfy133
jfy133 commented Sep 27, 2023
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jfy133 commented Sep 27, 2023

I confirm this works:

image

nextflow run ../main.nf -profile singularity,test --outdir ./results --skip_concoct false --skip_spadeshybrid --skip_prokka --skip_prodigal --run_gunc --bin_domain_classification

prototaxites
prototaxites approved these changes Sep 27, 2023
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LGTM 👍

CarsonJM
CarsonJM approved these changes Sep 27, 2023
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Looks good to me!

@jfy133 jfy133 merged commit e8316ab into dev Sep 27, 2023
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@jfy133 jfy133 deleted the fix-gunc-overwriting branch October 3, 2023 13:57
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
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@prototaxites prototaxites prototaxites approved these changes

@CarsonJM CarsonJM CarsonJM approved these changes

@maxibor maxibor Awaiting requested review from maxibor

@d4straub d4straub Awaiting requested review from d4straub

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@jfy133 @prototaxites @CarsonJM