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Dp24 pretext fix #283

Merged
merged 11 commits into from
Mar 20, 2024
Merged

Dp24 pretext fix #283

merged 11 commits into from
Mar 20, 2024

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DLBPointon
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  • Pretext updated to accept a fai file
  • Pretext config updated to remove a 'G' which is not an int and causes a crash in some cases (potentially large genomes which need to use the memory flag during processing).
  • gene alignment updated to re-introduce the meta.type to the file naming and stop the production of {name}_null.bed files which over write files of other types (which are all null).

@DLBPointon DLBPointon added bug Something isn't working enhancement New feature or request Release 1.1 Issues to be resolved for minor release 1.1 labels Mar 14, 2024
@DLBPointon DLBPointon added this to the Release 1 milestone Mar 14, 2024
@DLBPointon DLBPointon self-assigned this Mar 14, 2024
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github-actions bot commented Mar 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 59bc432

+| ✅ 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 2024-03-18 15:58:24

@DLBPointon DLBPointon mentioned this pull request Mar 14, 2024
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@DLBPointon
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Added the G back in, otherwise we get a segmentation fault at the samtools | pretext process We will have to keep this for now, but this very much needs investigation in the future. Some genomes will work with it, and others will fail due to the not a positive integer error which has been reported by both me and Will.

@yumisims
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I think I have figured out the bug, need to re-compile and re-generate the image, will update after GRC.

@DLBPointon DLBPointon linked an issue Mar 19, 2024 that may be closed by this pull request
Genomic data files are being out put as *null* #282
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@DLBPointon
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Also linked here: updating the module in nf-core for the fai file
nf-core/modules#5245

@DLBPointon DLBPointon merged commit c103783 into galaxy_dev Mar 20, 2024
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@DLBPointon DLBPointon deleted the dp24_pretext_fix branch March 20, 2024 13:37
@DLBPointon DLBPointon mentioned this pull request Mar 22, 2024
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@weaglesBio weaglesBio weaglesBio approved these changes

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Genomic data files are being out put as *null*
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@DLBPointon @yumisims @weaglesBio