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larger genome alignment should go to basement for now #258

Merged
merged 9 commits into from
Feb 16, 2024
Merged

larger genome alignment should go to basement for now #258

merged 9 commits into from
Feb 16, 2024

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yumisims
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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 Feb 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 024216d

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.2'
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • 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-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_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/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-02-16 16:16:12

@DLBPointon
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LGTM
I'll approve once it passes tests

@DLBPointon
Update base.config
024216d 
Replace {} with ()
@yumisims
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I knew it was something small!!

DLBPointon
DLBPointon requested changes Feb 16, 2024
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@DLBPointon DLBPointon left a comment

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Let's wait until the tests pass and then we can just commit this change and merge straight away

conf/base.config
time = { check_max( 10.h * task.attempt, 'time' ) }
}

// Standard parameters, covers most insecta
withName: '.*:.*:READ_COVERAGE:MINIMAP2_ALIGN' {
cpus = { check_max( 20 * 1, 'cpus' ) }
memory = { check_max( 50.GB * task.attempt, 'memory' ) }
time = { check_max( 20.h * task.attempt, 'time' ) }
time = { check_max( 1.h * (reference.size() < 1e9 ? 10 : reference.size() < 2.5e9 ? 30 : 300), 'time' ) }
//time = { check_max( 30.h * task.attempt, 'time' ) }
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Remove the unneeded time line

@yumisims yumisims merged commit 8da7da6 into galaxy_dev Feb 16, 2024
6 checks passed
@DLBPointon DLBPointon deleted the read_cov_resource branch February 16, 2024 17:19
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@DLBPointon DLBPointon DLBPointon requested changes

@weaglesBio weaglesBio weaglesBio approved these changes

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@yumisims @DLBPointon @weaglesBio