CWL Workflow: wgs alignment and tumor-only variant detection

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
bams	File[]
mills	File
docm_vcf	File
omni_vcf	File
vep_pick
dbsnp_vcf	File
reference	String
readgroups	String[]
sample_name	String
known_indels	File
qc_intervals	File
synonyms_file	File (Optional)
vep_cache_dir	String (Optional)
custom_gnomad_vcf	File (Optional)
summary_intervals	https://w3id.org/cwl/view/git/3ee63d8757c341ca98b3b46ec4782862ad19b710/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals	https://w3id.org/cwl/view/git/3ee63d8757c341ca98b3b46ec4782862ad19b710/definitions/types/labelled_file.yml#labelled_file[]
per_target_intervals	https://w3id.org/cwl/view/git/3ee63d8757c341ca98b3b46ec4782862ad19b710/definitions/types/labelled_file.yml#labelled_file[]
variant_detection_intervals	File
readcount_minimum_base_quality	Integer (Optional)
picard_metric_accumulation_level	String
readcount_minimum_mapping_quality	Integer (Optional)

ID	Runs	Label	Doc
detect_variants	tumor_only_detect_variants.cwl (Workflow)	Tumor-Only Detect Variants workflow
alignment_and_qc	wgs_alignment.cwl (Workflow)	wgs alignment with qc

ID	Type	Label	Doc
cram	File
final_tsv	File
final_vcf	File
flagstats	File
varscan_vcf	File
vep_summary	File
wgs_metrics	File
annotated_vcf	File
docm_gatk_vcf	File
gc_bias_metrics	File
summary_hs_metrics	File[]
insert_size_metrics	File
per_base_hs_metrics	File[]
verify_bam_id_depth	File
gc_bias_metrics_chart	File
insert_size_histogram	File
per_target_hs_metrics	File[]
verify_bam_id_metrics	File
gc_bias_metrics_summary	File
mark_duplicates_metrics	File
tumor_bam_readcount_tsv	File
alignment_summary_metrics	File
per_base_coverage_metrics	File[]
per_target_coverage_metrics	File[]