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Fix "Markdups process marks aligner output as markdups output incorrectly" #105

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merged 4 commits into from
Oct 30, 2024

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mvanniekerkHartwig
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Fixes issue #104 , by narrowing the wildcards for the markdups outputs to only include the actual output files from markdups.

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github-actions bot commented Oct 18, 2024

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 2.14.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@mvanniekerkHartwig mvanniekerkHartwig changed the base branch from master to dev October 18, 2024 09:53
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github-actions bot commented Oct 29, 2024

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 52064e8

+| ✅ 194 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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_genome_gtf 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 3.0.2
  • Run at 2024-10-29 23:43:17

@scwatts scwatts merged commit 2fcec6a into nf-core:dev Oct 30, 2024
6 checks passed
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2 participants