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Move BUSCO bash code a script#444

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jfy133 merged 7 commits intonf-core:devfrom
jfy133:busco-script
May 25, 2023
Merged

Move BUSCO bash code a script#444
jfy133 merged 7 commits intonf-core:devfrom
jfy133:busco-script

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@jfy133 jfy133 commented May 16, 2023

I just couldn't cope anymore with trying to debug pipelines during tests and having 100xs of a 300 line error msesage...

I've tested with -profile test and it produces output and no errors.

Resolves #393

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 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0dfad70

+| ✅ 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 2023-05-25 12:06:40

jfy133
jfy133 commented May 16, 2023
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prototaxites
prototaxites reviewed May 17, 2023
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Comment thread bin/run_busco.sh Outdated
@skrakau skrakau mentioned this pull request May 25, 2023
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skrakau commented May 25, 2023

Hi, isn't the output env variable most_spec_db missing?
I made a PR since I tested it: jfy133#15

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skrakau reviewed May 25, 2023
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Other than the missing output env variable, it looks good to me! One could add a proper handling of the input arguments with getopts, but not necessary in my opinion ...

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jfy133 commented May 25, 2023 •
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Other than the missing output env variable, it looks good to me! One could add a proper handling of the input arguments with getopts, but not necessary in my opinion ...

If you felt like doing that go ahead, I was trying simply for a one-to-one conversion here as I assumed the 'script' wouldn't really b e used outside of the pipeline 😬

@jfy133 jfy133 requested review from prototaxites and skrakau May 25, 2023 13:37
skrakau
skrakau approved these changes May 25, 2023
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LGTM :D

@jfy133 jfy133 merged commit 75b3b37 into nf-core:dev May 25, 2023
@jfy133 jfy133 deleted the busco-script branch May 25, 2023 13:40
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@skrakau skrakau skrakau approved these changes

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

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

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