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Hic opt #224

Merged
merged 49 commits into from
Feb 6, 2024
Merged

Hic opt #224

merged 49 commits into from
Feb 6, 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 Jan 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 291b055

+| ✅ 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 methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 2024-02-06 13:01:12

@gq1
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gq1 commented Jan 31, 2024

The runner name should be ubuntu2204-8c

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gq1 commented Jan 31, 2024

treeval/assets/github_testing/TreeValTinyFullTest.yaml

Line 34 in d81682f

synteny_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/synteny/

Does the line have the wrong path?

gq1
gq1 reviewed Feb 5, 2024
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.github/workflows/ci.yml Outdated
- name: Download containers
# Forcibly download repo on branch hic_opt and download SINGULARITY containers into the CACHE dir if not found
run: |
nf-core download sanger-tol/treeval --revision hic_opt --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system singularity
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This step pull all 35 sif image in advance before the run and it seems help lots .

After downloading, it seems we should run the pipeline differently according to the document. I never tried the nf-core download myself.

https://nf-co.re/tools#downloading-pipelines-for-offline-use

nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results # usual parameters here

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I can do that.

I've removed the checkout@v4 and how have it running the nf-core downloaded version. Has meant I've had to include another action to get branch names. See more on #234 .

@DLBPointon DLBPointon added the enhancement New feature or request label Feb 6, 2024
@DLBPointon DLBPointon added this to the Release 1 milestone Feb 6, 2024
@weaglesBio weaglesBio merged commit e89fe14 into galaxy_dev Feb 6, 2024
6 checks passed
@weaglesBio weaglesBio deleted the hic_opt branch February 6, 2024 13:43
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@yumisims @gq1 @DLBPointon @weaglesBio