Workflow: exome alignment and somatic variant detection

Fetched 2019-11-20 05:33:09 GMT
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Inputs

ID Type Title Doc
picard_metric_accumulation_level String
varscan_max_normal_freq Float (Optional)
qc_minimum_mapping_quality Integer (Optional)
tumor_bams File[]
per_base_intervals File
normal_readgroups String[]
target_intervals File
strelka_cpu_reserved Integer (Optional)
reference String
qc_minimum_base_quality Integer (Optional)
varscan_strand_filter Integer (Optional)
varscan_p_value Float (Optional)
annotate_coding_only Boolean (Optional)
variants_to_table_fields String[]
normal_bams File[]
mutect_artifact_detection_mode Boolean
varscan_min_var_freq Float (Optional)
variants_to_table_genotype_fields String[]
vep_to_table_fields String[]
custom_gnomad_vcf File (Optional)
omni_vcf File
vep_cache_dir String (Optional)
bqsr_intervals String[]
varscan_min_coverage Integer (Optional)
cle_vcf_filter Boolean
mills File
panel_of_normals_vcf File (Optional)
docm_vcf File
hgvs_annotation Boolean (Optional)
known_indels File
mutect_scatter_count Integer
per_target_intervals File
mutect_max_alt_allele_in_normal_fraction Float (Optional)
pindel_insert_size Integer
tumor_readgroups String[]
bait_intervals File
per_base_bait_intervals File
cosmic_vcf File (Optional)
dbsnp_vcf File
synonyms_file File (Optional)
mutect_max_alt_alleles_in_normal_count Integer (Optional)
interval_list File
per_target_bait_intervals File

Steps

ID Runs Label Doc
normal_alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc
tumor_alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc
detect_variants Detect Variants workflow

Outputs

ID Type Label Doc
normal_alignment_summary_metrics File
docm_filtered_vcf File
tumor_mark_duplicates_metrics File
normal_per_base_coverage_metrics File (Optional)
pindel_unfiltered_vcf File
normal_cram File
normal_hs_metrics File
normal_per_target_hs_metrics File (Optional)
tumor_cram File
tumor_bam_readcount_tsv File
tumor_verify_bam_id_depth File
tumor_flagstats File
normal_bam_readcount_tsv File
normal_verify_bam_id_depth File
normal_verify_bam_id_metrics File
final_filtered_vcf File
tumor_alignment_summary_metrics File
strelka_filtered_vcf File
final_vcf File
vep_summary File
mutect_filtered_vcf File
pindel_filtered_vcf File
tumor_hs_metrics File
normal_flagstats File
mutect_unfiltered_vcf File
tumor_per_target_coverage_metrics File (Optional)
tumor_per_target_hs_metrics File (Optional)
normal_mark_duplicates_metrics File
varscan_filtered_vcf File
strelka_unfiltered_vcf File
varscan_unfiltered_vcf File
normal_per_target_coverage_metrics File (Optional)
tumor_verify_bam_id_metrics File
tumor_per_base_hs_metrics File (Optional)
tumor_insert_size_metrics File
tumor_per_base_coverage_metrics File (Optional)
normal_insert_size_metrics File
normal_per_base_hs_metrics File (Optional)
final_tsv File
docm_unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/somatic_exome_workflow.cwl