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Add common nf-core/modules #19

Merged
merged 2 commits into from
Jul 16, 2021
Merged

Add common nf-core/modules #19

merged 2 commits into from
Jul 16, 2021

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abhi18av
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This PR adds the common nf-core/modules to the workflow.

There are many more tools which needs to be added, but as decided within the scope of #16 , we'll be adding them as local modules first.

@abhi18av abhi18av self-assigned this Jul 16, 2021
@abhi18av abhi18av added this to the v0.9 milestone Jul 16, 2021
@abhi18av abhi18av requested a review from Mxrcon July 16, 2021 14:26
@abhi18av abhi18av removed this from the v0.9 milestone Jul 16, 2021
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github-actions bot commented Jul 16, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a14d05f

+| ✅ 138 tests passed       |+
!| ❗  23 tests had warnings |!

❗ Test warnings:

  • 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in gwas.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 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
  • 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 check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet

✅ Tests passed:

Run details

  • nf-core/tools version 2.0.1
  • Run at 2021-07-16 14:45:21

Mxrcon
Mxrcon approved these changes Jul 16, 2021
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@Mxrcon Mxrcon left a comment •
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I think that these modules are ready for testing and we can proceed with the merge, also the tests seems fine. Just one thing: Are we going to add stubs for the processes?

Nice work on that @abhi18av!

@abhi18av
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abhi18av commented Jul 16, 2021 •
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@Mxrcon , stubs doesn't seem like a good way to go for the dev work since nf-core isn't relying on stubs so far.

If we want to do workflow testing based on stubs, we'd have to customize the modules/nf-core modules, which defeats the idea of using nf-core/modules.

Thanks for the review Davi 😊 !

@abhi18av abhi18av merged commit 820d8ea into nf-core:dev Jul 16, 2021
@abhi18av abhi18av deleted the abhinav/add-nf-modules branch July 16, 2021 18:01
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I think that these modules are ready for testing ...

The nf-core modules are already tested based on small datasets in that repo, therefore we can use them directly.

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Mxrcon commented Jul 16, 2021

ohh True! i forgot that, nf-core modules are ready and tested, our local modules that will need testing.

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