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First major dev PR #1

Merged
merged 14 commits into from
Jan 23, 2024
Merged

First major dev PR #1

merged 14 commits into from
Jan 23, 2024

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wsjung
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@wsjung wsjung commented Jan 23, 2024

First PR with semi-working rendition of omicsgenetraitassociation modules and subworkflows

wsjung and others added 14 commits January 21, 2024 20:59
@wsjung
updated nextflow.config with pipeline rename to omicsgenetraitassocia…
932f56b 
…tion
@wsjung
Template update for nf-core/tools version 2.11.1
ac5cc35
@wsjung
Merge branch 'TEMPLATE' into dev
43c9225 
synchronizing with nf-core template
@wsjung
added modules CMA, MMAP, and PASCAL
38fbb0d
@wsjung
fixed versions emit values for cma/main.nf and pascal/main.nf
e7a673b
@wsjung
added when directives to cma/main.nf
cc9b742
@wsjung
added MEA modules
4de0c29
@wsjung
pipeline works from CMA to MEA
6886178
@wsjung
added config for CMA and MEA configs in modules.config
966b810
@wsjung
updated .gitignore to exclude downloaded singularity images and added…
53e00b3 
… new config file for testing cma + mea modules
@wsjung
added temporary subworkflow CMA_SUBWORKFLOW which will later be modif…
ddd9790 
…ied to run CMA and MEA
@wsjung
commented out workflow initialization and validation steps for testing
7be6ed2
@wsjung
pascal/main.nf edited to extract tarball as nextflow does not support…
1e422f7 
… s3 glob support
@wsjung
fixed versions emit name
f582449
@wsjung wsjung merged commit 7692913 into nf-core:dev Jan 23, 2024
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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nf-core lint overall result: Failed ❌

Posted for pipeline commit f582449

+| ✅ 161 tests passed       |+
!| ❗  26 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • schema_params - Default value for param fasta invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • 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: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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 main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • 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 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowOmicsgenetraitassociation.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 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
  • schema_params - Schema param fasta not found from nextflow config

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-23 22:41:24

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@wsjung