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pipelines_aml_trio_cle_gathered.cwl

Travis CI User edited this page Feb 9, 2021 · 22 revisions

Documentation for aml_trio_cle_gathered.cwl

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Overview

gather AML trio outputs

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 File ['.tbi']
filter_docm_variants boolean?
filter_minimum_depth 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?
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_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[]
somalier_vcf File
output_dir string
disclaimer_version string
tumor_sample_name string
normal_sample_name string
disclaimer_text string?

Outputs

Name Label Description Type Secondary Files
final_outputs string[]

Steps

Name CWL Run
aml_trio pipelines/aml_trio_cle.cwl
gatherer tools/gatherer.cwl
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