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Add basic nf-core documentation #9

Merged
merged 12 commits into from
May 17, 2024
Merged

Add basic nf-core documentation #9

merged 12 commits into from
May 17, 2024

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scwatts
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@scwatts scwatts commented Mar 14, 2024

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github-actions bot commented Mar 14, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5e4ccdb

+| ✅ 175 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  53 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 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
  • 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 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]
  • 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 Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-17 00:06:12

@scwatts scwatts linked an issue Mar 14, 2024 that may be closed by this pull request
Complete basic nf-core documentation #5
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2 tasks
@scwatts scwatts added this to the Release 1.0.0 milestone Mar 14, 2024
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scwatts commented Mar 15, 2024

Force pushing after rebase on top of dev

@scwatts scwatts marked this pull request as ready for review March 15, 2024 06:11
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scwatts commented May 9, 2024

Force pushed to rebase on top of dev after merging latest template

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scwatts commented May 10, 2024

Another force push to rebase on top of dev

casslitch
casslitch reviewed May 13, 2024
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casslitch
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casslitch
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scwatts and others added 3 commits May 17, 2024 08:48
@scwatts @casslitch
Update docs/usage.md
b9b726f 
Co-authored-by: Cassie Litchfield <casslitch@gmail.com>
@scwatts @casslitch
Update docs/usage.md
6fb3d8d 
Co-authored-by: Cassie Litchfield <casslitch@gmail.com>
@scwatts
Further clarify MarkDups function, requirements
5e4ccdb
@scwatts scwatts merged commit 051952e into dev May 17, 2024
4 checks passed
@scwatts scwatts deleted the nf-core-documentation branch May 17, 2024 00:49
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@casslitch casslitch casslitch approved these changes

@charlesshale charlesshale charlesshale approved these changes

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Complete basic nf-core documentation
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@scwatts @charlesshale @casslitch