Workflow: Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

Fetched 2023-01-09 21:15:12 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table SelectVariants (GATK 4.1.8.1) variants_to_table_genotype_fields->variants_to_table genotype_fields expn_val expn_val pvacseq run pVACseq expn_val->pvacseq expn_val epitope_lengths_class_ii epitope_lengths_class_ii epitope_lengths_class_ii->pvacseq epitope_lengths_class_ii top_score_metric top_score_metric top_score_metric->pvacseq top_score_metric tdna_vaf tdna_vaf tdna_vaf->pvacseq tdna_vaf maximum_transcript_support_level maximum_transcript_support_level maximum_transcript_support_level->pvacseq maximum_transcript_support_level variants_to_table_fields variants_to_table_fields variants_to_table_fields->variants_to_table fields run_reference_proteome_similarity run_reference_proteome_similarity run_reference_proteome_similarity->pvacseq run_reference_proteome_similarity reference_fasta reference_fasta tumor_rna_bam_readcount bam_readcount workflow reference_fasta->tumor_rna_bam_readcount reference_fasta reference_fasta->variants_to_table reference normal_sample_name normal_sample_name normal_sample_name->pvacseq normal_sample_name tdna_cov tdna_cov tdna_cov->pvacseq tdna_cov normal_cov normal_cov normal_cov->pvacseq normal_cov minimum_fold_change minimum_fold_change minimum_fold_change->pvacseq minimum_fold_change gene_expression_file gene_expression_file add_gene_expression_data_to_vcf add expression info to vcf gene_expression_file->add_gene_expression_data_to_vcf expression_file epitope_lengths_class_i epitope_lengths_class_i epitope_lengths_class_i->pvacseq epitope_lengths_class_i trna_cov trna_cov trna_cov->pvacseq trna_cov readcount_minimum_base_quality readcount_minimum_base_quality readcount_minimum_base_quality->tumor_rna_bam_readcount min_base_quality netmhc_stab netmhc_stab netmhc_stab->pvacseq netmhc_stab fasta_size fasta_size fasta_size->pvacseq fasta_size additional_report_columns additional_report_columns additional_report_columns->pvacseq additional_report_columns downstream_sequence_length downstream_sequence_length downstream_sequence_length->pvacseq downstream_sequence_length alleles alleles alleles->pvacseq alleles rnaseq_bam rnaseq_bam rnaseq_bam->tumor_rna_bam_readcount bam transcript_expression_file transcript_expression_file add_transcript_expression_data_to_vcf add expression info to vcf transcript_expression_file->add_transcript_expression_data_to_vcf expression_file n_threads n_threads n_threads->pvacseq n_threads sample_name sample_name sample_name->tumor_rna_bam_readcount sample sample_name->add_transcript_expression_data_to_vcf sample_name sample_name->pvacseq sample_name add_tumor_rna_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf sample_name->add_tumor_rna_bam_readcount_to_vcf sample_name sample_name->add_gene_expression_data_to_vcf sample_name phased_proximal_variants_vcf phased_proximal_variants_vcf phased_proximal_variants_vcf->pvacseq phased_proximal_variants_vcf binding_threshold binding_threshold binding_threshold->pvacseq binding_threshold readcount_minimum_mapping_quality readcount_minimum_mapping_quality readcount_minimum_mapping_quality->tumor_rna_bam_readcount min_mapping_quality net_chop_method net_chop_method net_chop_method->pvacseq net_chop_method detect_variants_vcf detect_variants_vcf detect_variants_vcf->tumor_rna_bam_readcount vcf percentile_threshold percentile_threshold percentile_threshold->pvacseq percentile_threshold net_chop_threshold net_chop_threshold net_chop_threshold->pvacseq net_chop_threshold trna_vaf trna_vaf trna_vaf->pvacseq trna_vaf prediction_algorithms prediction_algorithms prediction_algorithms->pvacseq prediction_algorithms expression_tool expression_tool expression_tool->add_transcript_expression_data_to_vcf expression_tool expression_tool->add_gene_expression_data_to_vcf expression_tool allele_specific_binding_thresholds allele_specific_binding_thresholds vep_to_table_fields vep_to_table_fields add_vep_fields_to_table add VEP annotation to report vep_to_table_fields->add_vep_fields_to_table vep_fields peptide_sequence_length peptide_sequence_length exclude_nas exclude_nas exclude_nas->pvacseq exclude_nas normal_vaf normal_vaf normal_vaf->pvacseq normal_vaf pvacseq_predictions pvacseq_predictions annotated_vcf annotated_vcf annotated_tsv annotated_tsv tumor_rna_bam_readcount->add_tumor_rna_bam_readcount_to_vcf snv_bam_readcount_tsv tumor_rna_bam_readcount->add_tumor_rna_bam_readcount_to_vcf vcf tumor_rna_bam_readcount->add_tumor_rna_bam_readcount_to_vcf indel_bam_readcount_tsv add_transcript_expression_data_to_vcf->annotated_vcf index vcf index add_transcript_expression_data_to_vcf->index vcf pvacseq->pvacseq_predictions add_tumor_rna_bam_readcount_to_vcf->add_gene_expression_data_to_vcf vcf add_gene_expression_data_to_vcf->add_transcript_expression_data_to_vcf vcf variants_to_table->add_vep_fields_to_table tsv index->pvacseq input_vcf index->variants_to_table vcf index->add_vep_fields_to_table vcf add_vep_fields_to_table->annotated_tsv default1 "transcript" default1->add_transcript_expression_data_to_vcf data_type default2 "RNA" default2->add_tumor_rna_bam_readcount_to_vcf data_type default3 "gene" default3->add_gene_expression_data_to_vcf data_type default4 "pvacseq" default4->add_vep_fields_to_table prefix
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Inputs

ID Type Title Doc
alleles String[]
expn_val Float (Optional)
tdna_cov Integer (Optional)
tdna_vaf Float (Optional)
trna_cov Integer (Optional)
trna_vaf Float (Optional)
n_threads Integer (Optional)
fasta_size Integer (Optional)
normal_cov Integer (Optional)
normal_vaf Float (Optional)
rnaseq_bam File
exclude_nas Boolean (Optional)
netmhc_stab Boolean (Optional)
sample_name String (Optional)
expression_tool String (Optional)
net_chop_method
reference_fasta File
top_score_metric
binding_threshold Integer (Optional)
net_chop_threshold Float (Optional)
normal_sample_name String (Optional)
detect_variants_vcf File
minimum_fold_change Float (Optional)
vep_to_table_fields String[] (Optional)
gene_expression_file File
percentile_threshold Integer (Optional)
prediction_algorithms String[]
epitope_lengths_class_i Integer[] (Optional)
peptide_sequence_length Integer (Optional)
epitope_lengths_class_ii Integer[] (Optional)
variants_to_table_fields String[] (Optional)
additional_report_columns
downstream_sequence_length String (Optional)
transcript_expression_file File
phased_proximal_variants_vcf File (Optional)
readcount_minimum_base_quality Integer (Optional)
maximum_transcript_support_level
readcount_minimum_mapping_quality Integer (Optional)
run_reference_proteome_similarity Boolean (Optional)
variants_to_table_genotype_fields String[] (Optional)
allele_specific_binding_thresholds Boolean (Optional)

Steps

ID Runs Label Doc
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
pvacseq
../tools/pvacseq.cwl (CommandLineTool)
run pVACseq
variants_to_table
../tools/variants_to_table.cwl (CommandLineTool)
SelectVariants (GATK 4.1.8.1)
add_vep_fields_to_table
../tools/add_vep_fields_to_table.cwl (CommandLineTool)
add VEP annotation to report
tumor_rna_bam_readcount
bam_readcount.cwl (Workflow)
bam_readcount workflow
add_gene_expression_data_to_vcf
../tools/vcf_expression_annotator.cwl (CommandLineTool)
add expression info to vcf
add_tumor_rna_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf
add_transcript_expression_data_to_vcf
../tools/vcf_expression_annotator.cwl (CommandLineTool)
add expression info to vcf

Outputs

ID Type Label Doc
annotated_tsv File
annotated_vcf File
pvacseq_predictions Directory
Permalink: https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/subworkflows/pvacseq.cwl