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

Fetched 2021-01-09 04:24:44 GMT
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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)
epitope_lengths Integer[] (Optional)
expression_tool String (Optional)
net_chop_method https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/net_chop_methodd314563e-6275-4e25-a083-6f04451b1023 (Optional)
reference_fasta File
top_score_metric https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/top_score_metric11561a2d-32ae-4d14-9708-92f75789b328 (Optional)
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
prediction_algorithms String[]
peptide_sequence_length Integer (Optional)
variants_to_table_fields String[] (Optional)
additional_report_columns https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/additional_report_columnsd4783843-30b0-4532-96ea-73e1bddc7e26 (Optional)
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 https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/maximum_transcript_support_level5f5c422f-8405-42df-ae35-54c9a5e5738f (Optional)
readcount_minimum_mapping_quality Integer (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/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/pvacseq.cwl