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ASCC multi-assembly re-write #65

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ASCC multi-assembly re-write #65

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DLBPointon
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Unsure whether this will actually work, GitHub seems to thing the merge will be simple though.

Re-write adds:

  • Eeriks work on documentation
  • Support for multi-assembly runs using the samplesheet
  • organellar and genomic workflows
    • separate include/exclude flags for each, defaults to genomic workflow include "ALL" if not specified.

TODO:

  • Not right now, but we should continue to look at using Mahesh's pipeline nesting.

@DLBPointon DLBPointon added enhancement New feature or request Release 1 WIP Work In Progress labels Nov 13, 2024
@DLBPointon DLBPointon self-assigned this Nov 13, 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!

@DLBPointon DLBPointon mentioned this pull request Nov 13, 2024
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This was linked to issues Nov 13, 2024
Steps update #60
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Running the pipeline with primary assembly and haplotigs FASTA files at once #53
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@DLBPointon DLBPointon mentioned this pull request Nov 13, 2024
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@DLBPointon DLBPointon linked an issue Nov 13, 2024 that may be closed by this pull request
V1.1.0 - [REFACTOR] - Major refactor #44
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@DLBPointon DLBPointon mentioned this pull request Nov 13, 2024
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github-actions bot commented Nov 13, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit a4e87aa

+| ✅ 156 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗  20 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
  • 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: update the following command to include all required parameters for a minimal example
  • 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 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • 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 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
  • nfcore_yml - nf-core version in .nf-core.yml is not set to the latest version. Should be 3.0.2 but was 2.14.1

❔ 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/CONTRIBUTING.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/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • 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
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-14 13:25:42

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