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PR for MVP release! (for real) #36

Merged
merged 29 commits into from
Apr 10, 2024
Merged

PR for MVP release! (for real) #36

merged 29 commits into from
Apr 10, 2024

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nikhil
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@nikhil nikhil commented Apr 9, 2024

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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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nikhil commented Apr 9, 2024

Passes tests

[6b/ecd6b8] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:PHYLOWGS:PHYLOWGS_PARSECNVS ... [100%] 2 of 2 ✔
[8b/32c789] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:PHYLOWGS:PHYLOWGS_CREATEINPU... [100%] 2 of 2 ✔
[28/05a811] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:PHYLOWGS:PHYLOWGS_MULTIEVOLV... [100%] 2 of 2 ✔
[85/155fa1] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:PHYLOWGS:PHYLOWGS_WRITERESUL... [100%] 2 of 2 ✔
[1c/3872ec] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:NETMHCPAN (tumor_normal2)       [100%] 4 of 4 ✔
[96/822b5a] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:NEOANTIGENINPUT (tumor_normal2) [100%] 2 of 2 ✔
[1c/d55888] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:NEOANTIGEN_EDITING:NEOANTIGE... [100%] 2 of 2 ✔
[6d/24f8f8] process > MSKCC_NEOANTIGENPIPELINE:NEOANTIGENPIPELINE:NEOANTIGEN_EDITING:NEOANTIGE... [100%] 2 of 2 ✔
-[mskcc/neoantigenpipeline] Pipeline completed successfully-
Completed at: 09-Apr-2024 11:39:12
Duration    : 8m 3s
CPU hours   : 0.9
Succeeded   : 18

@nikhil nikhil closed this Apr 9, 2024
@nikhil nikhil reopened this Apr 9, 2024
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github-actions bot commented Apr 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 57edfaf

+| ✅ 145 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/NeoAntigen-Pipeline/NeoAntigen-Pipeline/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-10 19:23:59

@johnoooh
Change emit channel for pipeline
99aa7d1 
emit channel was still placeholder.  Should be good now.
johnoooh
johnoooh reviewed Apr 9, 2024
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workflows/neoantigenpipeline.nf Outdated
@@ -62,11 +76,13 @@ workflow NEOANTIGENPIPELINE {


emit:
versions = ch_versions // channel: [ path(versions.yml) ]
versions = ch_versions // channel: [ path(versions.yml) ]
neo_out = NEOANTIGENEDITING_COMPUTEFITNESS.out.annotated_output
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Changed this line in my last commit

@nikhil nikhil requested a review from johnoooh April 10, 2024 19:53
johnoooh
johnoooh approved these changes Apr 10, 2024
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Nice!

@johnoooh johnoooh merged commit ce3ce02 into dev Apr 10, 2024
4 checks passed
@nikhil nikhil deleted the test_profile_run branch April 10, 2024 22:30
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