pipelines_germline_wgs.cwl

Documentation for germline_wgs.cwl

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Overview

wgs alignment and germline variant detection

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
sequence	sequence: sequencing data and readgroup information	sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.	../types/sequence_data.yml#sequence_data[]
trimming			['../types/trimming_options.yml#trimming_options', 'null']
omni_vcf			File	['.tbi']
picard_metric_accumulation_level			string
emit_reference_confidence			{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']}
gvcf_gq_bands			string[]
intervals			{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
ploidy			int?
qc_intervals			File
variant_reporting_intervals			File
vep_cache_dir			['string', 'Directory']
vep_ensembl_assembly		genome assembly to use in vep. Examples: GRCh38 or GRCm38	string
vep_ensembl_version		ensembl version - Must be present in the cache directory. Example: 95	string
vep_ensembl_species		ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus	string
vep_plugins		array of plugins to use when running vep	string[]?
synonyms_file			File?
annotate_coding_only			boolean?
bqsr_known_sites		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.	File[]	['.tbi']
bqsr_intervals			string[]?
minimum_mapping_quality			int?
minimum_base_quality			int?
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
summary_intervals			../types/labelled_file.yml#labelled_file[]
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
cnvkit_diagram			boolean?
cnvkit_drop_low_coverage			boolean?
cnvkit_method			['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}]
cnvkit_reference_cnn			File?
cnvkit_scatter_plot			boolean?
cnvkit_male_reference			boolean?
cnvkit_vcf_name			string?
manta_call_regions			File?	['.tbi']
manta_non_wgs			boolean?
manta_output_contigs			boolean?
smoove_exclude_regions			File?
merge_max_distance			int
merge_min_svs			int
merge_same_type			boolean
merge_same_strand			boolean
merge_estimate_sv_distance			boolean
merge_min_sv_size			int
sv_filter_alt_abundance_percentage			double?
sv_filter_paired_count			int?
sv_filter_split_count			int?
cnv_filter_deletion_depth			double?
cnv_filter_duplication_depth			double?
variants_to_table_fields			string[]?
variants_to_table_genotype_fields			string[]?
vep_to_table_fields			string[]?
cnv_filter_min_size			int?
blocklist_bedpe			File?
disclaimer_text			string?

Outputs

Name	Label	Description	Type	Secondary Files
cram			File
mark_duplicates_metrics			File
insert_size_metrics			File
insert_size_histogram			File
alignment_summary_metrics			File
gc_bias_metrics			File
gc_bias_metrics_chart			File
gc_bias_metrics_summary			File
wgs_metrics			File
flagstats			File
verify_bam_id_metrics			File
verify_bam_id_depth			File
raw_vcf			File	['.tbi']
final_vcf			File	['.tbi']
filtered_vcf			File	['.tbi']
vep_summary			File
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
summary_hs_metrics			File[]
cn_diagram			File?
cn_scatter_plot			File?
tumor_antitarget_coverage			File
tumor_target_coverage			File
tumor_bin_level_ratios			File
tumor_segmented_ratios			File
cnvkit_vcf			File
cnvnator_cn_file			File
cnvnator_root			File
cnvnator_vcf			File
manta_diploid_variants			File?
manta_somatic_variants			File?
manta_all_candidates			File
manta_small_candidates			File
manta_tumor_only_variants			File?
smoove_output_variants			File
final_tsv			File
filtered_tsv			File
cnvkit_filtered_vcf			File
cnvnator_filtered_vcf			File
manta_filtered_vcf			File
smoove_filtered_vcf			File
survivor_merged_vcf			File
survivor_merged_annotated_tsv			File
bcftools_merged_vcf			File
bcftools_merged_annotated_tsv			File
bcftools_merged_filtered_annotated_tsv			File

Steps

Name	CWL Run
alignment_and_qc	pipelines/alignment_wgs.cwl
extract_freemix
detect_variants	subworkflows/germline_detect_variants.cwl
add_disclaimer_filtered_vcf	tools/add_string_at_line_bgzipped.cwl
index_disclaimer_filtered_vcf	tools/index_vcf.cwl
add_disclaimer_final_vcf	tools/add_string_at_line_bgzipped.cwl
index_disclaimer_final_vcf	tools/index_vcf.cwl
add_disclaimer_filtered_tsv	tools/add_string_at_line.cwl
add_disclaimer_final_tsv	tools/add_string_at_line.cwl
sv_detect_variants	subworkflows/single_sample_sv_callers.cwl
add_disclaimer_survivor_sv_vcf	tools/add_string_at_line_bgzipped.cwl
add_disclaimer_bcftools_sv_vcf	tools/add_string_at_line_bgzipped.cwl
add_disclaimer_survivor_sv_tsv	tools/add_string_at_line.cwl
add_disclaimer_bcftools_sv_tsv	tools/add_string_at_line.cwl
add_disclaimer_bcftools_filtered_sv_tsv	tools/add_string_at_line.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl