CWL Workflow: tnsnv-distr.cwl

This workflow is Open Source and may be reused according to the terms of: BSD 2-clause "Simplified" License

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

Inputs

ID	Type	Title	Doc
pon	File (Optional)
qcal	File[] (Optional)
dbsnp	File (Optional)
shard	String[]
cosmic	File (Optional)
threads	Integer (Optional)
interval	File (Optional)
input_bam	File[]
max_indel	Integer (Optional)
reference	File
detect_pon	Boolean (Optional)
pon_sample	String (Optional)
min_pir_mad	Double (Optional)
output_file	String
max_alt_mapq	Double (Optional)
tumor_sample	String (Optional)
min_base_qual	Integer (Optional)
min_tumor_lod	Double (Optional)
normal_sample	String (Optional)
max_mapq0_frac	Double (Optional)
min_normal_lod	Double (Optional)
min_pir_median	Double (Optional)
advanced_options	String[] (Optional)
power_allele_frac	Double (Optional)
contamination_frac	Double (Optional)
max_normal_alt_cnt	Integer (Optional)
max_read_clip_frac	Double (Optional)
min_init_tumor_lod	Double (Optional)
max_normal_alt_frac	Double (Optional)
max_normal_alt_qsum	Integer (Optional)
min_strand_bias_lod	Double (Optional)
min_dbsnp_normal_lod	Double (Optional)
min_strand_bias_power	Double (Optional)
min_tumor_allele_frac	Double (Optional)
min_cell_mutation_frac	Double (Optional)
min_normal_allele_frac	Double (Optional)

ID	Runs	Label	Doc
merge	../algo/tnsnv.cwl (CommandLineTool)
tnsnv	../algo/tnsnv.cwl (CommandLineTool)

ID	Type	Label	Doc
output	File