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Simplify geneset and synteny params in .yaml by using full paths. #340

Merged
merged 24 commits into from
Dec 9, 2024
Merged

Simplify geneset and synteny params in .yaml by using full paths. #340

merged 24 commits into from
Dec 9, 2024

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weaglesBio
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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).

Changed the input .yaml to accept lists of full paths for both synteny genomes and gene alignment genesets.

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github-actions bot commented Nov 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 233b326

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

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.0'
  • 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 2024-12-09 15:06:00

DLBPointon and others added 21 commits November 27, 2024 12:20
@DLBPointon
Nematode to fungi
7f6693f
@weaglesBio
Prettier
8043217
@weaglesBio
Merge branch 'dev' into tola406_genesetsyntenyyaml
96965a5
@DLBPointon
Updates
441c3e7
@DLBPointon
Re-add
a002b54
@DLBPointon
merqury fix
bca1939
@DLBPointon
Fudging the hash
ba1a458
@DLBPointon
Fudging the hash
d99fe23
@DLBPointon
Update modules again
b4b88df
@DLBPointon
Updates to Synteny to reflect Minimap2 update
163ffd6
@DLBPointon
Change to YAML_INPUT
b084e7c
@DLBPointon
Change SETUP from 1 to 2.14
c1e52e8
@DLBPointon
Change SETUP from 1 to 2.14
10212a8
@DLBPointon
Bump BAM2BED SORT to 2Gb as base
781615e
@DLBPointon
Adding VERSION information!
a929f2f
@DLBPointon
Making sure version information is printed
96f47fd
@DLBPointon
removing defaults
68a38a8
@DLBPointon
Update TreeValTinyFullTest.yaml
d87bed7
@DLBPointon
Update TreeValTinyFullTest.yaml
49f9ea5
@DLBPointon
Merge branch 'tola406_genesetsyntenyyaml' of https://github.com/sange…
4f211f7 
…r-tol/treeval into tola406_genesetsyntenyyaml
@DLBPointon
Updates for field value and PRETTER!
18688d6
@DLBPointon DLBPointon linked an issue Dec 9, 2024 that may be closed by this pull request
[1.3.0 - Ancient Puddlejumper] - Yet Another Module Update! #284
Open
@DLBPointon DLBPointon linked an issue Dec 9, 2024 that may be closed by this pull request
ERROR ~ No such variable: coverage_report #343
Open
@DLBPointon DLBPointon merged commit 436cd12 into dev Dec 9, 2024
6 checks passed
@DLBPointon DLBPointon deleted the tola406_genesetsyntenyyaml branch December 9, 2024 16:02
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@DLBPointon DLBPointon DLBPointon approved these changes

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ERROR ~ No such variable: coverage_report [1.3.0 - Ancient Puddlejumper] - Yet Another Module Update!
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@weaglesBio @DLBPointon