CWL Workflow: qc_workflow.cwl

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
hotspots	File
gene_list	File
run_tools	https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools
sample_id	String[]
patient_id	String[]
title_file	File
inputs_yaml	File
project_name	String
sample_class	String[]
standard_bams	File[]
waltz__params	https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/waltz.yaml#waltz__params
FP_config_file	File
pool_a_bed_file	File
pool_b_bed_file	File
reference_fasta	String
sample_directories	Directory[]
reference_fasta_fai	String
marianas_duplex_bams	File[]
A_on_target_positions	File
B_on_target_positions	File
marianas_simplex_bams	File[]
noise__good_positions_A	File
marianas_unfiltered_bams	File[]
pool_a_bed_file_exonlevel	File

ID	Runs	Doc
waltz_workflow	../waltz/waltz_workflow_all_bams.cwl (Workflow)
qc_workflow_wo_waltz	qc_workflow_wo_waltz.cwl (Workflow)	This workflow is intended to be used to test the QC module, without having to run the long waltz step
aggregate_picard_metrics	../../cwl_tools/expression_tools/combine_files_from_directories.cwl (ExpressionTool)	This tool will combine all files from each of the input directories, into one directory
collect_multiple_metrics	../../cwl_tools/picard/CollectMultipleMetrics.cwl (CommandLineTool)

ID	Type	Label	Doc
tables	Directory
picard_qc	Directory
combined_qc	Directory
hotspots_in_normals_data	File