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Longranger config #53

Merged
merged 4 commits into from
Aug 16, 2024
Merged

Longranger config #53

merged 4 commits into from
Aug 16, 2024

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muffato
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@muffato muffato commented Aug 16, 2024

Closes #48

Since we can't provide the longranger software we need to make that clear and provide instructions for people to use their own copy. In this PR, I move the container definition of longranger out of the base modules and into conf/longranger_lsf_sanger.config so that the modules are clear of Sanger config.
I also update the path to Singularity since it's different on our new LSF clusters.
Tested with

nextflow run path/to/sanger-tol/genomeassembly/ -profile test,sanger,singularity,longranger_lsf_sanger --outdir results_polishing --polishing_on

For external people, I added a section in docs/usage.md that explains how to install it.

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).

@muffato muffato added documentation Improvements or additions to documentation enhancement New feature or request labels Aug 16, 2024
@muffato muffato self-assigned this Aug 16, 2024
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github-actions bot commented Aug 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aab1b30

+| ✅ 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 2024-08-16 09:11:45

ksenia-krasheninnikova
ksenia-krasheninnikova approved these changes Aug 16, 2024
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@ksenia-krasheninnikova ksenia-krasheninnikova left a comment

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Looks good to me.

@muffato muffato merged commit 76d3fc9 into dev Aug 16, 2024
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@muffato muffato deleted the longranger_config branch August 16, 2024 09:35
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@ksenia-krasheninnikova ksenia-krasheninnikova ksenia-krasheninnikova approved these changes

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Broken singularity longranger image + help with organelles workflow
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@muffato @ksenia-krasheninnikova