pipelines_somatic_exome_nonhuman.cwl

Documentation for somatic_exome_nonhuman.cwl

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Overview

exome alignment and somatic variant detection

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
tumor_sequence	tumor_sequence: MT sequencing data and readgroup information	tumor_sequence represents the sequencing data for the MT sample 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[]
tumor_name	tumor_name: String specifying the name of the MT sample	tumor_name provides a string for what the MT sample will be referred to in the various outputs, for example the VCF files.	string?
normal_sequence	normal_sequence: WT sequencing data and readgroup information	normal_sequence represents the sequencing data for the WT sample 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[]
normal_name	normal_name: String specifying the name of the WT sample	normal_name provides a string for what the WT sample will be referred to in the various outputs, for example the VCF files.	string?
trimming			['../types/trimming_options.yml#trimming_options', 'null']
bait_intervals			File
target_intervals	target_intervals: interval_list file of targets used in the sequencing experiment	target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same.	File
target_interval_padding	target_interval_padding: number of bp flanking each target region in which to allow variant calls	The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions.	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[]
picard_metric_accumulation_level			string
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
strelka_cpu_reserved			int?
scatter_count		scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs	int
varscan_strand_filter			int?
varscan_min_coverage			int?
varscan_min_var_freq			float?
varscan_p_value			float?
varscan_max_normal_freq			float?
pindel_insert_size			int
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
synonyms_file			File?
annotate_coding_only			boolean?
vep_pick			['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}]
cle_vcf_filter			boolean
filter_somatic_llr_threshold		Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure.	float
filter_somatic_llr_tumor_purity		Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1	float
filter_somatic_llr_normal_contamination_rate		Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1	float
variants_to_table_fields			string[]
variants_to_table_genotype_fields			string[]
vep_to_table_fields			string[]
tumor_sample_name			string
normal_sample_name			string
cnvkit_target_average_size		approximate size of split target bins for CNVkit; if not set a suitable window size will be set by CNVkit automatically	int?

Outputs

Name	Label	Description	Type	Secondary Files
tumor_cram			File
tumor_mark_duplicates_metrics			File
tumor_insert_size_metrics			File
tumor_alignment_summary_metrics			File
tumor_hs_metrics			File
tumor_per_target_coverage_metrics			File[]
tumor_per_target_hs_metrics			File[]
tumor_per_base_coverage_metrics			File[]
tumor_per_base_hs_metrics			File[]
tumor_summary_hs_metrics			File[]
tumor_flagstats			File
normal_cram			File
normal_mark_duplicates_metrics			File
normal_insert_size_metrics			File
normal_alignment_summary_metrics			File
normal_hs_metrics			File
normal_per_target_coverage_metrics			File[]
normal_per_target_hs_metrics			File[]
normal_per_base_coverage_metrics			File[]
normal_per_base_hs_metrics			File[]
normal_summary_hs_metrics			File[]
normal_flagstats			File
mutect_unfiltered_vcf			File	['.tbi']
mutect_filtered_vcf			File	['.tbi']
strelka_unfiltered_vcf			File	['.tbi']
strelka_filtered_vcf			File	['.tbi']
varscan_unfiltered_vcf			File	['.tbi']
varscan_filtered_vcf			File	['.tbi']
pindel_unfiltered_vcf			File	['.tbi']
pindel_filtered_vcf			File	['.tbi']
final_vcf			File	['.tbi']
final_filtered_vcf			File	['.tbi']
final_tsv			File
vep_summary			File
tumor_snv_bam_readcount_tsv			File
tumor_indel_bam_readcount_tsv			File
normal_snv_bam_readcount_tsv			File
normal_indel_bam_readcount_tsv			File

Steps

Name	CWL Run
tumor_alignment_and_qc	pipelines/alignment_exome_nonhuman.cwl
normal_alignment_and_qc	pipelines/alignment_exome_nonhuman.cwl
pad_target_intervals	tools/interval_list_expand.cwl
detect_variants	pipelines/detect_variants_nonhuman.cwl
cnvkit	tools/cnvkit_batch.cwl
tumor_bam_to_cram	tools/bam_to_cram.cwl
tumor_index_cram	tools/index_cram.cwl
normal_bam_to_cram	tools/bam_to_cram.cwl
normal_index_cram	tools/index_cram.cwl