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ComBGC: Add functionality to screen whole sample directory (antismash) #258

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merged 7 commits into from
Apr 21, 2023
Merged

ComBGC: Add functionality to screen whole sample directory (antismash) #258

merged 7 commits into from
Apr 21, 2023

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jasmezz
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@jasmezz jasmezz commented Apr 17, 2023

Closes #256
Done: Support for multi-sample antismash output
To-do: The same for deepBGC and GECCO (when time, there is no need currently)

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/funcscan 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).

@jasmezz jasmezz added the enhancement Improvement for existing functionality label Apr 17, 2023
@jasmezz jasmezz requested a review from a team April 17, 2023 15:21
@jasmezz jasmezz changed the title Combgc new input param ComBGC: Add functionality to screen whole sample directory (antismash) Apr 17, 2023
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github-actions bot commented Apr 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b088681

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ 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 passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-20 15:48:13

louperelo
louperelo reviewed Apr 20, 2023
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Looks good in general. I just did not understand how the tools dict is working in case a --antismash_dir and no other tool is given.

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jasmezz commented Apr 20, 2023

Looks good in general. I just did not understand how the tools dict is working in case a --antismash_dir and no other tool is given.

No tool files = empty list, which will not populate the tools_provided list, thus show not up on the screen

@jasmezz jasmezz requested a review from louperelo April 20, 2023 14:19
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

louperelo
louperelo approved these changes Apr 20, 2023
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Looks good to me

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@nf-core-bot fix linting

@jasmezz jasmezz merged commit bc76195 into dev Apr 21, 2023
@jasmezz jasmezz deleted the combgc_new_input_param branch April 21, 2023 07:10
@jasmezz jasmezz mentioned this pull request Apr 21, 2023
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@jasmezz jasmezz restored the combgc_new_input_param branch April 21, 2023 09:05
@jasmezz jasmezz deleted the combgc_new_input_param branch April 21, 2023 09:07
@jasmezz jasmezz mentioned this pull request Apr 21, 2023
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