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Prepare genome subworkflow #84

Merged
merged 1 commit into from
Oct 18, 2023
Merged

Prepare genome subworkflow #84

merged 1 commit into from
Oct 18, 2023

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priyanka-surana
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This adds the optional masking subworkflow.

New boolean parameter: mask

The following tests work

nextflow run . -profile test,singularity -ansi-log false
nextflow run . -profile test_raw,singularity -ansi-log false
nextflow run . -profile test_raw,singularity -ansi-log false --mask true

@priyanka-surana priyanka-surana added the enhancement Improvement of the existing features label Sep 27, 2023
@priyanka-surana priyanka-surana added this to the 0.2.0 milestone Sep 27, 2023
@priyanka-surana priyanka-surana self-assigned this Sep 27, 2023
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github-actions bot commented Sep 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 44776b3

+| ✅ 129 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '0.2.0'

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.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/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.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-blobtoolkit_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-blobtoolkit_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_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-09-27 12:57:38

@muffato muffato changed the base branch from release to alignment September 30, 2023 12:54
alxndrdiaz
alxndrdiaz approved these changes Sep 30, 2023
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LGTM.

@priyanka-surana priyanka-surana merged commit 378ab70 into alignment Oct 18, 2023
6 checks passed
@priyanka-surana priyanka-surana deleted the prepare_genome branch October 18, 2023 09:18
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@alxndrdiaz alxndrdiaz alxndrdiaz approved these changes

@muffato muffato muffato approved these changes

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@priyanka-surana priyanka-surana

Labels
enhancement Improvement of the existing features
Projects
Genome After Party
Status: Done
Milestone
0.2.0
Development

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3 participants
@priyanka-surana @muffato @alxndrdiaz