pipelines_aml_trio_cle.cwl

Documentation for aml_trio_cle.cwl

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Overview

Replace legacy AML Trio Assay

Inputs

Name	Label	Description	Type	Secondary Files
reference			string
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			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			string?
followup_sequence			../types/sequence_data.yml#sequence_data[]
followup_name			string?
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[]
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']
emit_reference_confidence			{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']}
gvcf_gq_bands			string[]
intervals			{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
variant_reporting_intervals			File
picard_metric_accumulation_level			string
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
interval_list			File
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_region_file			File
pindel_insert_size			int
docm_vcf		Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)	File	['.tbi']
filter_docm_variants		Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls	boolean?
filter_minimum_depth			int?
vep_cache_dir			['string', 'Directory']
synonyms_file			File?
annotate_coding_only			boolean?
germline_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_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
somalier_vcf			File
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
germline_tsv_prefix			string?
germline_variants_to_table_fields			string[]
germline_variants_to_table_genotype_fields			string[]
germline_vep_to_table_fields			string[]
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_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_summary_hs_metrics			File[]
normal_flagstats			File
normal_verify_bam_id_metrics			File
normal_verify_bam_id_depth			File
followup_cram			File
followup_mark_duplicates_metrics			File
followup_insert_size_metrics			File
followup_alignment_summary_metrics			File
followup_hs_metrics			File
followup_summary_hs_metrics			File[]
followup_flagstats			File
followup_verify_bam_id_metrics			File
followup_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']
pindel_region_vcf			File	['.tbi']
tumor_snv_bam_readcount_tsv			File
tumor_indel_bam_readcount_tsv			File
normal_snv_bam_readcount_tsv			File
normal_indel_bam_readcount_tsv			File
followup_snv_bam_readcount_tsv			File
followup_indel_bam_readcount_tsv			File
tumor_final_vcf			File	['.tbi']
tumor_final_filtered_vcf			File	['.tbi']
tumor_final_tsv			File
tumor_vep_summary			File
germline_final_vcf			File	['.tbi']
germline_filtered_vcf			File	['.tbi']
germline_final_tsv			File
germline_filtered_tsv			File
somalier_concordance_metrics			File
somalier_concordance_statistics			File
alignment_stat_report			File
coverage_stat_report			File
full_variant_report			File

Steps

Name	CWL Run
normal_alignment_and_qc	pipelines/alignment_exome.cwl
tumor_alignment_and_qc	pipelines/alignment_exome.cwl
followup_alignment_and_qc	pipelines/alignment_exome.cwl
concordance	tools/concordance.cwl
tumor_detect_variants	pipelines/detect_variants.cwl
add_disclaimer_to_tumor_final_tsv	tools/add_string_at_line.cwl
add_disclaimer_version_to_tumor_final_tsv	tools/add_string_at_line.cwl
add_disclaimer_to_tumor_final_filtered_vcf	tools/add_string_at_line_bgzipped.cwl
add_disclaimer_version_to_tumor_final_filtered_vcf	tools/add_string_at_line_bgzipped.cwl
annotated_filter_vcf_index	tools/index_vcf.cwl
pindel_region	subworkflows/pindel_region.cwl
followup_bam_readcount	tools/bam_readcount.cwl
extract_freemix
germline_detect_variants	subworkflows/germline_detect_variants.cwl
add_disclaimer_to_germline_final_tsv	tools/add_string_at_line.cwl
add_disclaimer_version_to_germline_final_tsv	tools/add_string_at_line.cwl
alignment_report	tools/cle_aml_trio_report_alignment_stat.cwl
coverage_report	tools/cle_aml_trio_report_coverage_stat.cwl
full_report	tools/cle_aml_trio_report_full_variants.cwl
add_disclaimer_to_full_variant_report	tools/add_string_at_line.cwl
add_disclaimer_version_to_full_variant_report	tools/add_string_at_line.cwl
normal_bam_to_cram	tools/bam_to_cram.cwl
normal_index_cram	tools/index_cram.cwl
tumor_bam_to_cram	tools/bam_to_cram.cwl
tumor_index_cram	tools/index_cram.cwl
followup_bam_to_cram	tools/bam_to_cram.cwl
followup_index_cram	tools/index_cram.cwl