Workflow: gather AML trio outputs

Fetched 2023-01-09 23:09:47 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs bait_intervals bait_intervals aml_trio Replace legacy AML Trio Assay bait_intervals->aml_trio bait_intervals varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->aml_trio varscan_min_var_freq vep_to_table_fields vep_to_table_fields vep_to_table_fields->aml_trio vep_to_table_fields vep_ensembl_assembly vep_ensembl_assembly vep_ensembl_assembly->aml_trio vep_ensembl_assembly variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->aml_trio variants_to_table_genotype_fields tumor_sample_name tumor_sample_name tumor_sample_name->aml_trio tumor_sample_name bqsr_intervals bqsr_intervals bqsr_intervals->aml_trio bqsr_intervals germline_coding_only germline_coding_only germline_coding_only->aml_trio germline_coding_only cle_vcf_filter cle_vcf_filter cle_vcf_filter->aml_trio cle_vcf_filter filter_minimum_depth filter_minimum_depth filter_minimum_depth->aml_trio filter_minimum_depth filter_docm_variants filter_docm_variants filter_docm_variants->aml_trio filter_docm_variants normal_sample_name normal_sample_name normal_sample_name->aml_trio normal_sample_name interval_list interval_list interval_list->aml_trio interval_list intervals intervals intervals->aml_trio intervals germline_vep_to_table_fields germline_vep_to_table_fields germline_vep_to_table_fields->aml_trio germline_vep_to_table_fields qc_minimum_mapping_quality qc_minimum_mapping_quality qc_minimum_mapping_quality->aml_trio qc_minimum_mapping_quality per_target_intervals per_target_intervals per_target_intervals->aml_trio per_target_intervals vep_pick vep_pick vep_pick->aml_trio vep_pick followup_name followup_name followup_name->aml_trio followup_name pindel_region_file pindel_region_file pindel_region_file->aml_trio pindel_region_file tumor_name tumor_name tumor_name->aml_trio tumor_name gvcf_gq_bands gvcf_gq_bands gvcf_gq_bands->aml_trio gvcf_gq_bands germline_variants_to_table_genotype_fields germline_variants_to_table_genotype_fields germline_variants_to_table_genotype_fields->aml_trio germline_variants_to_table_genotype_fields per_base_intervals per_base_intervals per_base_intervals->aml_trio per_base_intervals bqsr_known_sites bqsr_known_sites bqsr_known_sites->aml_trio bqsr_known_sites vep_custom_annotations vep_custom_annotations vep_custom_annotations->aml_trio vep_custom_annotations scatter_count scatter_count scatter_count->aml_trio scatter_count germline_variants_to_table_fields germline_variants_to_table_fields germline_variants_to_table_fields->aml_trio germline_variants_to_table_fields variants_to_table_fields variants_to_table_fields variants_to_table_fields->aml_trio variants_to_table_fields tumor_sequence tumor_sequence: MT sequencing data and readgroup information tumor_sequence->aml_trio tumor_sequence annotate_coding_only annotate_coding_only annotate_coding_only->aml_trio annotate_coding_only strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->aml_trio strelka_cpu_reserved disclaimer_text disclaimer_text disclaimer_text->aml_trio disclaimer_text picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->aml_trio picard_metric_accumulation_level qc_minimum_base_quality qc_minimum_base_quality qc_minimum_base_quality->aml_trio qc_minimum_base_quality varscan_min_coverage varscan_min_coverage varscan_min_coverage->aml_trio varscan_min_coverage summary_intervals summary_intervals summary_intervals->aml_trio summary_intervals normal_name normal_name normal_name->aml_trio normal_name followup_sequence followup_sequence followup_sequence->aml_trio followup_sequence docm_vcf docm_vcf docm_vcf->aml_trio docm_vcf varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->aml_trio varscan_max_normal_freq variant_reporting_intervals variant_reporting_intervals variant_reporting_intervals->aml_trio variant_reporting_intervals vep_cache_dir vep_cache_dir vep_cache_dir->aml_trio vep_cache_dir germline_tsv_prefix germline_tsv_prefix germline_tsv_prefix->aml_trio germline_tsv_prefix output_dir output_dir gatherer gatherer output_dir->gatherer output_dir somalier_vcf somalier_vcf somalier_vcf->aml_trio somalier_vcf varscan_strand_filter varscan_strand_filter varscan_strand_filter->aml_trio varscan_strand_filter pindel_insert_size pindel_insert_size pindel_insert_size->aml_trio pindel_insert_size normal_sequence normal_sequence: WT sequencing data and readgroup information normal_sequence->aml_trio normal_sequence omni_vcf omni_vcf omni_vcf->aml_trio omni_vcf varscan_p_value varscan_p_value varscan_p_value->aml_trio varscan_p_value disclaimer_version disclaimer_version disclaimer_version->aml_trio disclaimer_version vep_ensembl_species vep_ensembl_species vep_ensembl_species->aml_trio vep_ensembl_species target_intervals target_intervals target_intervals->aml_trio target_intervals vep_ensembl_version vep_ensembl_version vep_ensembl_version->aml_trio vep_ensembl_version reference reference reference->aml_trio reference synonyms_file synonyms_file synonyms_file->aml_trio synonyms_file emit_reference_confidence emit_reference_confidence emit_reference_confidence->aml_trio emit_reference_confidence final_outputs final_outputs gatherer->final_outputs aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files aml_trio->gatherer all_files
Workflow as SVG
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  • Inputs/Outputs

Inputs

ID Type Title Doc
docm_vcf File
omni_vcf File
vep_pick
intervals 53e78779fa60906434a33eec79e25fbf[]
reference String
output_dir String
tumor_name String (Optional)
normal_name String (Optional)
somalier_vcf File
followup_name String (Optional)
gvcf_gq_bands String[]
interval_list File
scatter_count Integer

scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs

synonyms_file File (Optional)
vep_cache_dir Directory
bait_intervals File
bqsr_intervals String[]
cle_vcf_filter Boolean
tumor_sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] 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.

disclaimer_text String (Optional)
normal_sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] 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.

varscan_p_value Float (Optional)
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

target_intervals File
followup_sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[]
summary_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
tumor_sample_name String
disclaimer_version String
normal_sample_name String
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
pindel_insert_size Integer
pindel_region_file File
germline_tsv_prefix String (Optional)
vep_ensembl_species String

ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus

vep_ensembl_version String

ensembl version - Must be present in the cache directory. Example: 95

vep_to_table_fields String[]
annotate_coding_only Boolean (Optional)
filter_docm_variants Boolean (Optional)
filter_minimum_depth Integer (Optional)
germline_coding_only Boolean (Optional)
per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
strelka_cpu_reserved Integer (Optional)
varscan_min_coverage Integer (Optional)
varscan_min_var_freq Float (Optional)
vep_ensembl_assembly String

genome assembly to use in vep. Examples: GRCh38 or GRCm38

varscan_strand_filter Integer (Optional)
vep_custom_annotations https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]

custom type, check types directory for input format

qc_minimum_base_quality Integer (Optional)
varscan_max_normal_freq Float (Optional)
variants_to_table_fields String[]
emit_reference_confidence
qc_minimum_mapping_quality Integer (Optional)
variant_reporting_intervals File
germline_vep_to_table_fields String[]
picard_metric_accumulation_level String
germline_variants_to_table_fields String[]
variants_to_table_genotype_fields String[]
germline_variants_to_table_genotype_fields String[]

Steps

ID Runs Label Doc
aml_trio
aml_trio_cle.cwl (Workflow)
Replace legacy AML Trio Assay
gatherer
../tools/gatherer.cwl (CommandLineTool)

Outputs

ID Type Label Doc
final_outputs String[]
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/aml_trio_cle_gathered.cwl