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Use pipe with closure #1119

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This PR uses an experimental pipe + closure syntax from nextflow-io/nextflow#3423 to simplify the pipeline logic where appropriate.

Not a high priority thing, just something cool I wanted to try. It's failing at the moment with some cryptic error. But more importantly, it didn't add a ton of simplification to begin with, since most processes have multiple inputs and outputs and are guarded by if statements. I'll leave it here for now for anyone who is interested.

PR checklist

  • 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).

@bentsherman
Use pipe with closure
cb5040d 
Signed-off-by: Ben Sherman <[email protected]>
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github-actions bot commented Nov 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cb5040d

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.13.0
  • 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
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-16 21:34:04

@bentsherman bentsherman closed this May 1, 2024
@bentsherman bentsherman deleted the pipe-with-closure branch May 1, 2024 03:18
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