CWL Workflow: exome alignment and 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
dbsnp_vcf	File
reference	String
readgroups	String[]
sample_name	String
known_indels	File
synonyms_file	File (Optional)
vep_cache_dir	String (Optional)
bait_intervals	File
bqsr_intervals	String[] (Optional)
hgvs_annotation	Boolean (Optional)
varscan_p_value	Float (Optional)
target_intervals	File
custom_gnomad_vcf	File (Optional)
varscan_min_reads	Integer (Optional)
per_base_intervals	File
vep_to_table_fields	String[] (Optional)
annotate_coding_only	Boolean (Optional)
per_target_intervals	File
varscan_min_coverage	Integer (Optional)
varscan_min_var_freq	Float (Optional)
varscan_strand_filter	Integer (Optional)
per_base_bait_intervals	File
qc_minimum_base_quality	Integer (Optional)
variants_to_table_fields	String[] (Optional)
per_target_bait_intervals	File
qc_minimum_mapping_quality	Integer (Optional)
readcount_minimum_base_quality	Integer (Optional)
picard_metric_accumulation_level	String
readcount_minimum_mapping_quality	Integer (Optional)
variants_to_table_genotype_fields	String[] (Optional)
maximum_population_allele_frequency	Float (Optional)

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

ID	Type	Label	Doc
cram	File
final_tsv	File
final_vcf	File
flagstats	File
hs_metrics	File
varscan_vcf	File
vep_summary	File
annotated_vcf	File
docm_gatk_vcf	File
insert_size_metrics	File
per_base_hs_metrics	File (Optional)
verify_bam_id_depth	File
insert_size_histogram	File
per_target_hs_metrics	File (Optional)
verify_bam_id_metrics	File
mark_duplicates_metrics	File
tumor_bam_readcount_tsv	File
alignment_summary_metrics	File
per_base_coverage_metrics	File (Optional)
per_target_coverage_metrics	File (Optional)