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hap1/hap2 scaffolding #51

Merged
merged 16 commits into from
Sep 6, 2024
Merged

hap1/hap2 scaffolding #51

merged 16 commits into from
Sep 6, 2024

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ksenia-krasheninnikova
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@ksenia-krasheninnikova ksenia-krasheninnikova commented Aug 15, 2024 •
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Implements https://jira.sanger.ac.uk/browse/TOLA-315

When hifiasm in hic mode is switched on hap1/hap2 contigs are scaffolded up.
Before this PR was implemented the phased assemblies were only contig-level. Now the phased hifiasm contigs are scaffolded up and usual QC checks are run for them.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Aug 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cbc319e

+| ✅ 130 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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.

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_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
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • 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 ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomeassembly/genomeassembly/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-09-06 12:16:58

@gq1
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gq1 commented Aug 30, 2024

I can see all module and workflow changes, can't see any related documentation updated, can you add?
I don't know much about these workflows, all looks fine for me.

@ksenia-krasheninnikova
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@gq1 Thanks. Docs have been updated.

gq1
gq1 reviewed Sep 6, 2024
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@ksenia-krasheninnikova ksenia-krasheninnikova merged commit 115b833 into dev Sep 6, 2024
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@gq1 gq1 gq1 approved these changes

@yumisims yumisims yumisims approved these changes

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