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Update CITATIONS.md #31

Merged
merged 1 commit into from
May 15, 2024
Merged

Update CITATIONS.md #31

merged 1 commit into from
May 15, 2024

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scwatts
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@scwatts scwatts commented May 14, 2024

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@scwatts scwatts requested a review from charlesshale May 14, 2024 02:32
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 311c1bf

+| ✅ 175 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  57 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.3.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • 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
  • system_exit - System.exit in main.nf: System.exit(1) [line 45]
  • system_exit - System.exit in main.nf: System.exit(1) [line 46]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]
  • system_exit - System.exit in WorkflowOncoanalyser.groovy: System.exit(1) [line 62]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 29]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 39]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 47]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 55]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 63]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 68]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 84]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 89]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 108]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 113]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 121]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 182]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 264]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 276]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 284]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 291]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 299]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 314]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 335]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 346]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 355]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 385]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 118]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 125]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 132]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 146]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 156]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 161]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 174]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 190]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 199]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 210]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 220]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-14 02:34:07

@scwatts scwatts merged commit 7ed732c into dev May 15, 2024
4 checks passed
@scwatts scwatts deleted the update-citations branch May 15, 2024 00:41
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale