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Rename bwa-mem2 index variables #34

Merged
merged 3 commits into from
May 17, 2024
Merged

Rename bwa-mem2 index variables #34

merged 3 commits into from
May 17, 2024

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scwatts
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@scwatts scwatts commented May 16, 2024

  • more clearly differentiates bwa-mem2 and BWA indexes since these are two distinct pieces of software
  • adjusted remote paths accordingly; edited existing 24.1 version since it is not yet tied to an oncoanalyser release
  • also included: STAR index placeholder creation for stub runs

@scwatts scwatts requested a review from charlesshale May 16, 2024 06:55
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scwatts commented May 17, 2024

Force pushing on top of dev in order to adjust bwa-mem2 variable names/URLs in new documentation

@scwatts scwatts force-pushed the improve-bwa-mem2-index-name branch from 138b02e to 5ea55f5 Compare May 17, 2024 00:52
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github-actions bot commented May 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 112d239

+| ✅ 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 265]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 277]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 285]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 292]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 300]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 315]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 336]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 347]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 356]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 386]
  • 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 00:55:14

@scwatts scwatts merged commit a88b036 into dev May 17, 2024
4 checks passed
@scwatts scwatts deleted the improve-bwa-mem2-index-name branch May 17, 2024 01:03
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale