pipelines_somatic_exome_cle.cwl

Documentation for somatic_exome_cle.cwl

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Overview

exome alignment and somatic variant detection for cle purpose

Inputs

Name	Label	Description	Type	Secondary Files
reference			string
tumor_sequence			../types/sequence_data.yml#sequence_data[]
tumor_name			string?
normal_sequence			../types/sequence_data.yml#sequence_data[]
normal_name			string?
mills			File	['.tbi']
known_indels			File	['.tbi']
dbsnp_vcf			File	['.tbi']
bqsr_intervals			string[]
bait_intervals			File
target_intervals			File
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[]
omni_vcf			File	['.tbi']
picard_metric_accumulation_level			string
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
interval_list			File
strelka_cpu_reserved			int?
mutect_scatter_count			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
docm_vcf			File	['.tbi']
filter_docm_variants			boolean?
filter_minimum_depth			int?
vep_cache_dir			string
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
variants_to_table_fields			string[]
variants_to_table_genotype_fields			string[]
vep_to_table_fields			string[]
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
somalier_vcf			File
disclaimer_text			string?
disclaimer_version			string
tumor_sample_name			string
normal_sample_name			string

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
tumor_verify_bam_id_metrics			File
tumor_verify_bam_id_depth			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
normal_verify_bam_id_metrics			File
normal_verify_bam_id_depth			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']
docm_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
somalier_concordance_metrics			File
somalier_concordance_statistics			File