CWL Workflow: exome alignment and germline 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	Doc
bams	File[]
mills	File
omni_vcf	File
dbsnp_vcf	File
intervals	24a5d8b81cf6ae4ceee1eec8f0af2d0e[]
reference	String
readgroups	String[]
known_indels	File
vep_assembly	String	Used to explicitly define which assembly version to use; required when there are two or more in the same directory
gvcf_gq_bands	String[]
synonyms_file	File (Optional)
vep_cache_dir	String
bait_intervals	File
bqsr_intervals	String[] (Optional)
target_intervals	File
custom_gnomad_vcf	File (Optional)
summary_intervals	https://w3id.org/cwl/view/git/1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68/definitions/types/labelled_file.yml#labelled_file[]
custom_clinvar_vcf	File (Optional)
per_base_intervals	https://w3id.org/cwl/view/git/1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68/definitions/types/labelled_file.yml#labelled_file[]
annotate_coding_only	Boolean (Optional)
per_target_intervals	https://w3id.org/cwl/view/git/1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68/definitions/types/labelled_file.yml#labelled_file[]
qc_minimum_base_quality	Integer (Optional)
emit_reference_confidence	String
qc_minimum_mapping_quality	Integer (Optional)
picard_metric_accumulation_level	String

ID	Runs	Label
index_cram	../tools/index_cram.cwl (CommandLineTool)	samtools index cram
bam_to_cram	../tools/bam_to_cram.cwl (CommandLineTool)	BAM to CRAM conversion
detect_variants	../subworkflows/germline_detect_variants.cwl (Workflow)	exome alignment and germline variant detection
extract_freemix	germline_exome.cwl#extract_freemix/d06138a5-5e34-4835-9b5c-f84d8aa714b1 (ExpressionTool)
alignment_and_qc	exome_alignment.cwl (Workflow)	exome alignment with qc

ID	Type	Label	Doc
cram	File
gvcf	File[]
final_vcf	File
flagstats	File
coding_vcf	File
hs_metrics	File
limited_vcf	File
vep_summary	File
summary_hs_metrics	File[]
insert_size_metrics	File
per_base_hs_metrics	File[]
verify_bam_id_depth	File
insert_size_histogram	File
per_target_hs_metrics	File[]
verify_bam_id_metrics	File
mark_duplicates_metrics	File
alignment_summary_metrics	File
per_base_coverage_metrics	File[]
per_target_coverage_metrics	File[]