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RGI add parameter to save json files #252

Merged
merged 7 commits into from Apr 14, 2023
Merged

RGI add parameter to save json files #252

merged 7 commits into from Apr 14, 2023

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Darcy220606
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@Darcy220606 Darcy220606 commented Mar 29, 2023 •
edited

In this PR:

  • CHANGE: RGI outputs by default only .txt and have added the arg_rgi_savejson parameter to give the user the option to save it as part of the RGI output dir if required.
  • REASON: We noticed that RGI outputs HUGE .json files, which are quite bulky and are not required downstream in the pipeline.
  • CLOSES issue Optionally keep RGI json output #245

TODO

  • Usage Documentation in docs/usage.md is updated. NOTYET!!!
  • Output Documentation in docs/output.md is updated. NOTYET!!
  • CHANGELOG.md is updated. NOTYET!!
  • README.md is updated (including new tool citations and authors/contributors).

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>).

jfy133
jfy133 reviewed Mar 29, 2023
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CHANGEOG update?

@Darcy220606
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Have to catch the train, will do the documentation part later when im back :)

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github-actions bot commented Mar 29, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7d1b977

+| ✅ 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 2023-04-14 13:40:23

louperelo
louperelo approved these changes Mar 30, 2023
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LGTM

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jasmezz
jasmezz requested changes Apr 3, 2023
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jasmezz
jasmezz requested changes Apr 3, 2023
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@jfy133 jfy133 linked an issue Apr 4, 2023 that may be closed by this pull request
Optionally keep RGI json output #245
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@jfy133 jfy133 marked this pull request as draft April 4, 2023 10:52
Darcy220606 and others added 2 commits April 13, 2023 18:34
@Darcy220606
update changelog and output.md
c51412b
@Darcy220606 @jasmezz
Update nextflow_schema.json
1bca438 
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
@Darcy220606 Darcy220606 marked this pull request as ready for review April 13, 2023 16:37
jasmezz
jasmezz approved these changes Apr 14, 2023
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Thanks for the updates!
Why are bakta tests failing though? Also for PR #242 it looks like. Could you check if we can fix them here or in another PR (run local test and check for errors)?

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Darcy220606 and others added 2 commits April 14, 2023 12:10
@Darcy220606
Merge branch 'nf-core:master' into rgi_json_save
3b21dab
@Darcy220606 @jasmezz
Add reviewer suggestions
7d1b977 
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
@Darcy220606 Darcy220606 merged commit 91c9f8c into nf-core:dev Apr 14, 2023
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This was referenced Apr 20, 2023
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@louperelo louperelo louperelo approved these changes

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Optionally keep RGI json output
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@Darcy220606 @jfy133 @louperelo @jasmezz