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Generate genome #21

Merged
merged 2 commits into from
Aug 17, 2022
Merged

Generate genome #21

merged 2 commits into from
Aug 17, 2022

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DLBPointon
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PR checklist

GENERATE_GENOME is a subworkflow that generates a .genome file used in multiple other workflows.

This will replace INPUT_CHECK (which is not needed).

This being merged to main early as it is a basal SW.

This has been tested locally and shown to work.

@DLBPointon DLBPointon self-assigned this Aug 17, 2022
@DLBPointon DLBPointon merged commit 1b01884 into master Aug 17, 2022
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a4f4bd3

+| ✅ 147 tests passed       |+
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in treeval.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-08-17 11:12:35

@DLBPointon DLBPointon deleted the generate_genome branch September 15, 2022 11:18
DLBPointon added a commit that referenced this pull request Sep 7, 2023
@DLBPointon
Merge pull request #21 from DLBPointon/generate_genome
f8b715f 
Generate genome
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