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Dp24 gc content #28

Merged
merged 20 commits into from
Oct 10, 2023
Merged

Dp24 gc content #28

merged 20 commits into from
Oct 10, 2023

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DLBPointon
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Adds GC_CONTENT and GENERATE_GENOME as well as respective modules and scripts

@DLBPointon DLBPointon added this to the Release 1 milestone Oct 5, 2023
@DLBPointon DLBPointon self-assigned this Oct 5, 2023
@DLBPointon DLBPointon mentioned this pull request Oct 5, 2023
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github-actions bot commented Oct 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5e01a76

+| ✅ 125 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • 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 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 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 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 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 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
  • system_exit - System.exit in WorkflowAscc.groovy: System.exit(1) [line 18]

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-10 13:50:03

@DLBPointon DLBPointon requested a review from weaglesBio October 5, 2023 12:04
weaglesBio
weaglesBio reviewed Oct 5, 2023
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Minor changes to version tracking, otherwise good.

modules/local/gc_content.nf Show resolved Hide resolved
subworkflows/local/generate_genome.nf Show resolved Hide resolved
workflows/ascc.nf Show resolved Hide resolved
@DLBPointon DLBPointon requested a review from weaglesBio October 5, 2023 15:26
weaglesBio
weaglesBio reviewed Oct 5, 2023
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Version mixes are okay, pandas and python version should be included in the versions.yml in gc_content.nf

@DLBPointon
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Version mixes are okay, pandas and python version should be included in the versions.yml in gc_content.nf

I'll get on that Monday, I'll copy it across to other modules too

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@weaglesBio
Morning Will,
Only get_lineages_kraken actually uses pandas, so I've corrected the container in use as well as the version data output by the modules.

@DLBPointon DLBPointon requested a review from weaglesBio October 9, 2023 09:43
@DLBPointon DLBPointon requested a review from yumisims October 10, 2023 10:58
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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!

@DLBPointon DLBPointon merged commit 5d5f200 into dev Oct 10, 2023
6 checks passed
@DLBPointon DLBPointon deleted the dp24_gc_content branch October 10, 2023 13:58
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@yumisims yumisims yumisims approved these changes

@weaglesBio weaglesBio Awaiting requested review from weaglesBio

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@DLBPointon @yumisims @weaglesBio