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Prepping for pixelator 1.0 release #75

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wants to merge 8 commits into from
Closed

Prepping for pixelator 1.0 release #75

wants to merge 8 commits into from

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johandahlberg
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This PR contains changes that prepare nf-core/pixelator for the 1.0 release of pixelator. The main difference is that the collapse and graph steps will now output parquet files. It also fixes a bunch of spelling errors.

For now, since the new pixelator version is not release in order for the tests to pass you need to add: --pixelator_container ghcr.io/pixelgentechnologies/pixelator:dev. We should update the default container once everything is in place in biocontainers.

Linting currently fails, which I guess is because we have note yet updated to the new nf-core templates?

PR checklist

  • This comment contains a description of changes (with reason).
  • 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 11, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 69d55fe

+| ✅ 171 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌  13 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.outdir is set as ./results in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is null/pipeline_info in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-pixelator_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-pixelator_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-pixelator_logo_dark.png does not match the template
  • files_unchanged - .prettierignore does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-08 15:27:11

@fbdtemme fbdtemme force-pushed the EXE-1100-prepping-for-pixelator-0.16 branch from 0a2b595 to 87a2aa1 Compare January 22, 2024 13:07
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fbdtemme commented Mar 4, 2024

This work is continuing in another branch so we will close this one.

@fbdtemme fbdtemme closed this Mar 4, 2024
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@fbdtemme fbdtemme Awaiting requested review from fbdtemme

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@johandahlberg @fbdtemme