Delivery Sub-workflowΒΆ

Workflow File:

https://github.com/NCI-CGR/GwasQcPipeline/blob/default/src/cgr_gwas_qc/workflow/sub_workflows/delivery.smk

Config Options: see The config.yml for more details

  • user_files.output_pattern

  • workflow_params.lims_upload

  • workflow_params.lims_output_dir

  • workflow_params.time_start

Major Outputs:

  • delivery/samples.bed

  • delivery/samples.bim

  • delivery/samples.fam

  • delivery/SampleUsedforSubject.csv

  • delivery/subjects.bed

  • delivery/subjects.bim

  • delivery/subjects.fam

  • delivery/HWP.zip

  • delivery/*AnalysisManifest*.csv

  • delivery/*QC_Report*.docx

  • delivery/*QC_Report*.xlsx

  • files_for_lab/*all_sample_qc*.csv

  • files_for_lab/*LimsUpload*.csv

  • files_for_lab/*Identifiler*.csv

  • files_for_lab/*KnownReplicates*.csv

  • files_for_lab/*UnknownReplicates*.csv

The delivery workflow mostly just copies files to the correct location in either delivery/ or files_for_lab/. It also generates the QC report (*.docx) and QC report table (*.xlsx). If this lims_upload options is set then it will copy *LimsUpload*.csv to the designated lims_output_dir.