TheiaProk TB: new VCF output and modification to the coverage report #245
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* updated VCF output file renaming in kSNP3 task (#207) * updated VCF output file renaming in kSNP3 task; also added 1 new File output and change the output names to be more descriptive * ksnp3 task:changed VCF file names to be predictable; split 2 ksnp3 options to 2 lines for readability; added new string output "ksnp3_vcf_ref_samplename" to capture sample within cluster to use for snp calling * added new string output to ksnp3 workflow "ksnp3_vcf_ref_samplename" * reduce unnecessary logging in MIDAS task (#210) * made untar/decompression of midas database quiet since it produces 41k lines of output. also made the 2 mv commands verbose (but it's only 2 lines!) * update CI * expose tbprofiler parameters as inputs in merlin * input spelling --------- Co-authored-by: Curtis Kapsak <kapsakcj@gmail.com>
kevinlibuit
reviewed
Dec 29, 2023
tasks/task_versioning.wdl
Outdated
| @@ -9,7 +9,7 @@ task version_capture { | |||
| volatile: true | |||
| } | |||
| command { | |||
| PHB_Version="PHB v1.2.1" | |||
| PHB_Version="PHB v1.2.1: smw-tb-2023-10-25-dev branch" | |||
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Will need to modify before merge
kevinlibuit
approved these changes
Dec 29, 2023
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DO NOT MAKE CHANGES TO THIS BRANCH!!!!!!!
closes #283
I recognize Frank made a branch that alters some parameters, so those might need to be incorporated, but these were the latest iteration of changes I made to the TB analysis pathway.
🛠️ Changes Being Made
This PR:
Impacted Workflows/Tasks
Tasks:
tasks/species_typing/task_tbp_parser.wdltasks/species_typing/task_tbprofiler.wdlWorkflows:
workflows/theiaprok/wf_theiaprok_illumina_pe.wdlworkflows/theiaprok/wf_theiaprok_illumina_se.wdlworkflows/theiaprok/wf_theiaprok_ont.wdlworkflows/utiltiies/wf_merlin_magic.wdl🧠 Context and Rationale
Changes were requested by users.
📋 Workflow/Task Steps
Inputs
No inputs were changed
Outputs
New output:
tbprofiler_output_vcfImpacted Outputs
Modified outputs:
tbp_parser_coverage_reporttbp_parser_dockertbp_parser_versionAdditional changes were made in the
tbp-parseroutput files due to changes associated with the updated Docker image.🧪 Testing
Locally
Terra
Scenarios for Reviewer to Test
🔬 Quality checks
Pull Request (PR) checklist: