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Fix directory shadowing symlinks #53

Merged
merged 1 commit into from
Jun 4, 2024
Merged

Fix directory shadowing symlinks #53

merged 1 commit into from
Jun 4, 2024

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scwatts
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@scwatts scwatts commented Jun 4, 2024

  • when oncoanalyser runs under a directory path containing a space, directory shadowing fails causing a pipeline crash
  • this bug impacts both the GRIDSS assemble and GRIDSS call process
  • changes made in this PR allow proper handling of paths containing spaces for directory shadowing

@scwatts scwatts requested a review from charlesshale June 4, 2024 00:08
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github-actions bot commented Jun 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 85765b1

+| ✅ 177 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-04 00:09:45

@scwatts scwatts merged commit 67275f5 into dev Jun 4, 2024
4 checks passed
@scwatts scwatts deleted the fix-directory-shadowing-symlinks branch June 4, 2024 00:27
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale