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No req input.csv #454

Merged
merged 2 commits into from
Nov 17, 2021
Merged

No req input.csv #454

merged 2 commits into from
Nov 17, 2021

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nickhsmith
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@nickhsmith nickhsmith commented Nov 17, 2021 •
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nf-core/sarek pull request

This is to address the issue #451. @maxulysse did a good job at pointing out the expected style for the params.step options. During this confusion, I realized that for sarek/dev both nextflow_schema.json and lib/WorkflowMain.groovy there is an explicit requirement to include params.input

However workflows/sarek.nf includes a case finding step (lines 48-60) designed to handle the different steps and their corresponding pre-built csv files. In order to recapture the utility of the params.step functionality, I have removed these explicit requirements.

In the lines 48-60 of workflows/sarek.nf covers the following cases

  • input.csv designated
    • valid input.csv
      • nothing's changed. uses step to only do steps
    • invalid input.csv
      • nothing's changed. will throw errors as any bad input.csv will
  • no input.csv
    • valid step: mapping
      • throw error. mapping step must have a designated input.csv (desired)
    • valid step: prepare_recalibration -> annotate
      • try to find the prebuilt csv file to restart the job
    • invalid step:
      • throw an error detailing an unknown step (desired)

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
    • Usage documentation is way out of date

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github-actions bot commented Nov 17, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7898b0f

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-17 15:52:48

maxulysse
maxulysse approved these changes Nov 17, 2021
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Love that

@maxulysse maxulysse merged commit 4d7678f into nf-core:dev Nov 17, 2021
@nickhsmith nickhsmith deleted the no_req_input.csv branch November 24, 2021 13:44
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@maxulysse maxulysse maxulysse approved these changes

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@nickhsmith @maxulysse