/
immuno.cwl
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immuno.cwl
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#/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Immunotherapy Workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
#rnaseq inputs
reference_index:
type: File #this requires an extra file with the basename
secondaryFiles: [".1.ht2", ".2.ht2", ".3.ht2", ".4.ht2", ".5.ht2", ".6.ht2", ".7.ht2", ".8.ht2"]
reference_annotation:
type: File
rna_bams:
type: File[]
rna_readgroups:
type: string[]
read_group_fields:
type:
type: array
items:
type: array
items: string
sample_name:
type: string
trimming_adapters:
type: File
trimming_adapter_trim_end:
type: string
trimming_adapter_min_overlap:
type: int
trimming_max_uncalled:
type: int
trimming_min_readlength:
type: int
kallisto_index:
type: File
gene_transcript_lookup_table:
type: File
strand:
type:
- "null"
- type: enum
symbols: ["first", "second", "unstranded"]
refFlat:
type: File
ribosomal_intervals:
type: File
reference_transcriptome:
type: File
#somatic inputs
reference: string
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_name:
type: string?
default: 'tumor'
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_name:
type: string?
default: 'normal'
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]
bait_intervals:
type: File
target_intervals:
type: File
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
qc_minimum_mapping_quality:
type: int?
default: 0
qc_minimum_base_quality:
type: int?
default: 0
interval_list:
type: File
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
panel_of_normals_vcf:
type: File?
secondaryFiles: [.tbi]
strelka_cpu_reserved:
type: int?
default: 8
mutect_scatter_count:
type: int
mutect_artifact_detection_mode:
type: boolean
default: false
mutect_max_alt_allele_in_normal_fraction:
type: float?
mutect_max_alt_alleles_in_normal_count:
type: int?
varscan_strand_filter:
type: int?
default: 0
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.05
varscan_p_value:
type: float?
default: 0.99
varscan_max_normal_freq:
type: float?
pindel_insert_size:
type: int
default: 400
docm_vcf:
type: File
secondaryFiles: [.tbi]
filter_docm_variants:
type: boolean?
default: true
vep_cache_dir:
type: string
vep_ensembl_assembly:
type: string
doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
vep_ensembl_version:
type: string
doc: "ensembl version - Must be present in the cache directory. Example: 95"
vep_ensembl_species:
type: string
doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
cle_vcf_filter:
type: boolean
default: false
variants_to_table_fields:
type: string[]
default: [CHROM,POS,ID,REF,ALT,set,AC,AF]
variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
vep_to_table_fields:
type: string[]
default: [HGVSc,HGVSp]
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
manta_call_regions:
type: File?
secondaryFiles: [.tbi]
manta_non_wgs:
type: boolean?
default: true
manta_output_contigs:
type: boolean?
somalier_vcf:
type: File
#germline inputs
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
gatk_haplotypecaller_intervals:
type:
type: array
items:
type: array
items: string
optitype_name:
type: string?
#phase_vcf inputs
reference_dict:
type: File
#pvacseq inputs
readcount_minimum_base_quality:
type: int?
readcount_minimum_mapping_quality:
type: int?
prediction_algorithms:
type: string[]
epitope_lengths:
type: int[]?
binding_threshold:
type: int?
allele_specific_binding_thresholds:
type: boolean?
minimum_fold_change:
type: float?
peptide_sequence_length:
type: int?
top_score_metric:
type:
- "null"
- type: enum
symbols: ["lowest", "median"]
additional_report_columns:
type:
- "null"
- type: enum
symbols: ["sample_name"]
fasta_size:
type: int?
downstream_sequence_length:
type: string?
exclude_nas:
type: boolean?
phased_proximal_variants_vcf:
type: File?
secondaryFiles: ['.tbi']
maximum_transcript_support_level:
type:
- "null"
- type: enum
symbols: ["1", "2", "3", "4", "5"]
normal_cov:
type: int?
tdna_cov:
type: int?
trna_cov:
type: int?
normal_vaf:
type: float?
tdna_vaf:
type: float?
trna_vaf:
type: float?
expn_val:
type: float?
net_chop_method:
type:
- "null"
- type: enum
symbols: ["cterm", "20s"]
net_chop_threshold:
type: float?
netmhc_stab:
type: boolean?
pvacseq_threads:
type: int?
immuno_tumor_sample_name:
type: string
immuno_normal_sample_name:
type: string
outputs:
final_bam:
type: File
outputSource: rnaseq/final_bam
secondaryFiles: [.bai]
stringtie_transcript_gtf:
type: File
outputSource: rnaseq/stringtie_transcript_gtf
stringtie_gene_expression_tsv:
type: File
outputSource: rnaseq/stringtie_gene_expression_tsv
transcript_abundance_tsv:
type: File
outputSource: rnaseq/transcript_abundance_tsv
transcript_abundance_h5:
type: File
outputSource: rnaseq/transcript_abundance_h5
gene_abundance:
type: File
outputSource: rnaseq/gene_abundance
metrics:
type: File
outputSource: rnaseq/metrics
chart:
type: File
outputSource: rnaseq/chart
fusion_evidence:
type: File
outputSource: rnaseq/fusion_evidence
unfiltered_fusion_seqs:
type: File
outputSource: rnaseq/unfiltered_fusion_seqs
unfiltered_fusions_json:
type: File
outputSource: rnaseq/unfiltered_fusions_json
filtered_fusion_seqs:
type: File
outputSource: rnaseq/filtered_fusion_seqs
filtered_fusions_json:
type: File
outputSource: rnaseq/filtered_fusions_json
final_fusion_calls:
type: File
outputSource: rnaseq/final_fusion_calls
tumor_cram:
type: File
outputSource: somatic/tumor_cram
tumor_mark_duplicates_metrics:
type: File
outputSource: somatic/tumor_mark_duplicates_metrics
tumor_insert_size_metrics:
type: File
outputSource: somatic/tumor_insert_size_metrics
tumor_alignment_summary_metrics:
type: File
outputSource: somatic/tumor_alignment_summary_metrics
tumor_hs_metrics:
type: File
outputSource: somatic/tumor_hs_metrics
tumor_per_target_coverage_metrics:
type: File[]
outputSource: somatic/tumor_per_target_coverage_metrics
tumor_per_target_hs_metrics:
type: File[]
outputSource: somatic/tumor_per_target_hs_metrics
tumor_per_base_coverage_metrics:
type: File[]
outputSource: somatic/tumor_per_base_coverage_metrics
tumor_per_base_hs_metrics:
type: File[]
outputSource: somatic/tumor_per_base_hs_metrics
tumor_summary_hs_metrics:
type: File[]
outputSource: somatic/tumor_summary_hs_metrics
tumor_flagstats:
type: File
outputSource: somatic/tumor_flagstats
tumor_verify_bam_id_metrics:
type: File
outputSource: somatic/tumor_verify_bam_id_metrics
tumor_verify_bam_id_depth:
type: File
outputSource: somatic/tumor_verify_bam_id_depth
normal_cram:
type: File
outputSource: somatic/normal_cram
normal_mark_duplicates_metrics:
type: File
outputSource: somatic/normal_mark_duplicates_metrics
normal_insert_size_metrics:
type: File
outputSource: somatic/normal_insert_size_metrics
normal_alignment_summary_metrics:
type: File
outputSource: somatic/normal_alignment_summary_metrics
normal_hs_metrics:
type: File
outputSource: somatic/normal_hs_metrics
normal_per_target_coverage_metrics:
type: File[]
outputSource: somatic/normal_per_target_coverage_metrics
normal_per_target_hs_metrics:
type: File[]
outputSource: somatic/normal_per_target_hs_metrics
normal_per_base_coverage_metrics:
type: File[]
outputSource: somatic/normal_per_base_coverage_metrics
normal_per_base_hs_metrics:
type: File[]
outputSource: somatic/normal_per_base_hs_metrics
normal_summary_hs_metrics:
type: File[]
outputSource: somatic/normal_summary_hs_metrics
normal_flagstats:
type: File
outputSource: somatic/normal_flagstats
normal_verify_bam_id_metrics:
type: File
outputSource: somatic/normal_verify_bam_id_metrics
normal_verify_bam_id_depth:
type: File
outputSource: somatic/normal_verify_bam_id_depth
mutect_unfiltered_vcf:
type: File
outputSource: somatic/mutect_unfiltered_vcf
secondaryFiles: [.tbi]
mutect_filtered_vcf:
type: File
outputSource: somatic/mutect_filtered_vcf
secondaryFiles: [.tbi]
strelka_unfiltered_vcf:
type: File
outputSource: somatic/strelka_unfiltered_vcf
secondaryFiles: [.tbi]
strelka_filtered_vcf:
type: File
outputSource: somatic/strelka_filtered_vcf
secondaryFiles: [.tbi]
varscan_unfiltered_vcf:
type: File
outputSource: somatic/varscan_unfiltered_vcf
secondaryFiles: [.tbi]
varscan_filtered_vcf:
type: File
outputSource: somatic/varscan_filtered_vcf
secondaryFiles: [.tbi]
pindel_unfiltered_vcf:
type: File
outputSource: somatic/pindel_unfiltered_vcf
secondaryFiles: [.tbi]
pindel_filtered_vcf:
type: File
outputSource: somatic/pindel_filtered_vcf
secondaryFiles: [.tbi]
docm_filtered_vcf:
type: File
outputSource: somatic/docm_filtered_vcf
secondaryFiles: [.tbi]
somatic_final_vcf:
type: File
outputSource: somatic/final_vcf
secondaryFiles: [.tbi]
final_filtered_vcf:
type: File
outputSource: somatic/final_filtered_vcf
secondaryFiles: [.tbi]
final_tsv:
type: File
outputSource: somatic/final_tsv
somatic_vep_summary:
type: File
outputSource: somatic/vep_summary
tumor_snv_bam_readcount_tsv:
type: File
outputSource: somatic/tumor_snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: somatic/tumor_indel_bam_readcount_tsv
normal_snv_bam_readcount_tsv:
type: File
outputSource: somatic/normal_snv_bam_readcount_tsv
normal_indel_bam_readcount_tsv:
type: File
outputSource: somatic/normal_indel_bam_readcount_tsv
intervals_antitarget:
type: File?
outputSource: somatic/intervals_antitarget
intervals_target:
type: File?
outputSource: somatic/intervals_target
normal_antitarget_coverage:
type: File
outputSource: somatic/normal_antitarget_coverage
normal_target_coverage:
type: File
outputSource: somatic/normal_target_coverage
reference_coverage:
type: File?
outputSource: somatic/reference_coverage
cn_diagram:
type: File?
outputSource: somatic/cn_diagram
cn_scatter_plot:
type: File?
outputSource: somatic/cn_scatter_plot
tumor_antitarget_coverage:
type: File
outputSource: somatic/tumor_antitarget_coverage
tumor_target_coverage:
type: File
outputSource: somatic/tumor_target_coverage
tumor_bin_level_ratios:
type: File
outputSource: somatic/tumor_bin_level_ratios
tumor_segmented_ratios:
type: File
outputSource: somatic/tumor_segmented_ratios
diploid_variants:
type: File?
outputSource: somatic/diploid_variants
secondaryFiles: [.tbi]
somatic_variants:
type: File?
outputSource: somatic/somatic_variants
secondaryFiles: [.tbi]
all_candidates:
type: File
outputSource: somatic/all_candidates
secondaryFiles: [.tbi]
small_candidates:
type: File
outputSource: somatic/small_candidates
secondaryFiles: [.tbi]
tumor_only_variants:
type: File?
outputSource: somatic/tumor_only_variants
secondaryFiles: [.tbi]
somalier_concordance_metrics:
type: File
outputSource: somatic/somalier_concordance_metrics
somalier_concordance_statistics:
type: File
outputSource: somatic/somalier_concordance_statistics
cram:
type: File
outputSource: germline/cram
mark_duplicates_metrics:
type: File
outputSource: germline/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: germline/insert_size_metrics
insert_size_histogram:
type: File
outputSource: germline/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: germline/alignment_summary_metrics
hs_metrics:
type: File
outputSource: germline/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: germline/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: germline/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: germline/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: germline/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: germline/summary_hs_metrics
flagstats:
type: File
outputSource: germline/flagstats
verify_bam_id_metrics:
type: File
outputSource: germline/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: germline/verify_bam_id_depth
gvcf:
type: File[]
outputSource: germline/gvcf
germline_final_vcf:
type: File
outputSource: germline/final_vcf
secondaryFiles: [.tbi]
coding_vcf:
type: File
outputSource: germline/coding_vcf
secondaryFiles: [.tbi]
limited_vcf:
type: File
outputSource: germline/limited_vcf
secondaryFiles: [.tbi]
germline_vep_summary:
type: File
outputSource: germline/vep_summary
optitype_tsv:
type: File
outputSource: germline/optitype_tsv
optitype_plot:
type: File
outputSource: germline/optitype_plot
phased_vcf:
type: File
outputSource: phase_vcf/phased_vcf
secondaryFiles: [.tbi]
allele_string:
type: string[]
outputSource: extract_alleles/allele_string
annotated_vcf:
type: File
outputSource: pvacseq/annotated_vcf
annotated_tsv:
type: File
outputSource: pvacseq/annotated_tsv
mhc_i_all_epitopes:
type: File?
outputSource: pvacseq/mhc_i_all_epitopes
mhc_i_filtered_epitopes:
type: File?
outputSource: pvacseq/mhc_i_filtered_epitopes
mhc_i_ranked_epitopes:
type: File?
outputSource: pvacseq/mhc_i_ranked_epitopes
mhc_ii_all_epitopes:
type: File?
outputSource: pvacseq/mhc_ii_all_epitopes
mhc_ii_filtered_epitopes:
type: File?
outputSource: pvacseq/mhc_ii_filtered_epitopes
mhc_ii_ranked_epitopes:
type: File?
outputSource: pvacseq/mhc_ii_ranked_epitopes
combined_all_epitopes:
type: File?
outputSource: pvacseq/combined_all_epitopes
combined_filtered_epitopes:
type: File?
outputSource: pvacseq/combined_filtered_epitopes
combined_ranked_epitopes:
type: File?
outputSource: pvacseq/combined_ranked_epitopes
steps:
rnaseq:
run: rnaseq.cwl
in:
reference_index: reference_index
reference_annotation: reference_annotation
instrument_data_bams: rna_bams
read_group_id: rna_readgroups
read_group_fields: read_group_fields
sample_name: sample_name
trimming_adapters: trimming_adapters
trimming_adapter_trim_end: trimming_adapter_trim_end
trimming_adapter_min_overlap: trimming_adapter_min_overlap
trimming_max_uncalled: trimming_max_uncalled
trimming_min_readlength: trimming_min_readlength
kallisto_index: kallisto_index
gene_transcript_lookup_table: gene_transcript_lookup_table
strand: strand
refFlat: refFlat
ribosomal_intervals: ribosomal_intervals
reference_transcriptome: reference_transcriptome
species: vep_ensembl_species
assembly: vep_ensembl_assembly
out:
[final_bam, stringtie_transcript_gtf, stringtie_gene_expression_tsv, transcript_abundance_tsv, transcript_abundance_h5, gene_abundance, metrics, chart, fusion_evidence, unfiltered_fusion_seqs, unfiltered_fusions_json, filtered_fusion_seqs, filtered_fusions_json, final_fusion_calls]
somatic:
run: somatic_exome.cwl
in:
reference: reference
tumor_sequence: tumor_sequence
tumor_name: tumor_name
normal_sequence: normal_sequence
normal_name: normal_name
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
interval_list: interval_list
cosmic_vcf: cosmic_vcf
panel_of_normals_vcf: panel_of_normals_vcf
strelka_cpu_reserved: strelka_cpu_reserved
mutect_scatter_count: mutect_scatter_count
mutect_artifact_detection_mode: mutect_artifact_detection_mode
mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count
varscan_strand_filter: varscan_strand_filter
varscan_min_coverage: varscan_min_coverage
varscan_min_var_freq: varscan_min_var_freq
varscan_p_value: varscan_p_value
varscan_max_normal_freq: varscan_max_normal_freq
pindel_insert_size: pindel_insert_size
docm_vcf: docm_vcf
filter_docm_variants: filter_docm_variants
vep_cache_dir: vep_cache_dir
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
vep_pick: vep_pick
cle_vcf_filter: cle_vcf_filter
variants_to_table_fields: variants_to_table_fields
variants_to_table_genotype_fields: variants_to_table_genotype_fields
vep_to_table_fields: vep_to_table_fields
custom_gnomad_vcf: custom_gnomad_vcf
custom_clinvar_vcf: custom_clinvar_vcf
manta_call_regions: manta_call_regions
manta_non_wgs: manta_non_wgs
manta_output_contigs: manta_output_contigs
somalier_vcf: somalier_vcf
out:
[tumor_cram,tumor_mark_duplicates_metrics,tumor_insert_size_metrics,tumor_alignment_summary_metrics,tumor_hs_metrics,tumor_per_target_coverage_metrics,tumor_per_target_hs_metrics,tumor_per_base_coverage_metrics,tumor_per_base_hs_metrics,tumor_summary_hs_metrics,tumor_flagstats,tumor_verify_bam_id_metrics,tumor_verify_bam_id_depth,normal_cram,normal_mark_duplicates_metrics,normal_insert_size_metrics,normal_alignment_summary_metrics,normal_hs_metrics,normal_per_target_coverage_metrics,normal_per_target_hs_metrics,normal_per_base_coverage_metrics,normal_per_base_hs_metrics,normal_summary_hs_metrics,normal_flagstats,normal_verify_bam_id_metrics,normal_verify_bam_id_depth,mutect_unfiltered_vcf,mutect_filtered_vcf,strelka_unfiltered_vcf,strelka_filtered_vcf,varscan_unfiltered_vcf,varscan_filtered_vcf,pindel_unfiltered_vcf,pindel_filtered_vcf,docm_filtered_vcf,final_vcf,final_filtered_vcf,final_tsv,vep_summary,tumor_snv_bam_readcount_tsv,tumor_indel_bam_readcount_tsv,normal_snv_bam_readcount_tsv,normal_indel_bam_readcount_tsv,intervals_antitarget,intervals_target,normal_antitarget_coverage,normal_target_coverage,reference_coverage,cn_diagram,cn_scatter_plot,tumor_antitarget_coverage,tumor_target_coverage,tumor_bin_level_ratios,tumor_segmented_ratios,diploid_variants,somatic_variants,all_candidates,small_candidates,tumor_only_variants,somalier_concordance_metrics,somalier_concordance_statistics]
germline:
run: germline_exome_hla_typing.cwl
in:
reference: reference
sequence: normal_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: gatk_haplotypecaller_intervals
vep_cache_dir: vep_cache_dir
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
custom_gnomad_vcf: custom_gnomad_vcf
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
custom_clinvar_vcf: custom_clinvar_vcf
optitype_name: optitype_name
out:
[cram,mark_duplicates_metrics,insert_size_metrics,insert_size_histogram,alignment_summary_metrics,hs_metrics,per_target_coverage_metrics,per_target_hs_metrics,per_base_coverage_metrics,per_base_hs_metrics,summary_hs_metrics,flagstats,verify_bam_id_metrics,verify_bam_id_depth,gvcf,final_vcf,coding_vcf,limited_vcf,vep_summary,optitype_tsv,optitype_plot]
rename_somatic_vcf_tumor_sample:
run: ../tools/replace_vcf_sample_name.cwl
in:
input_vcf: somatic/final_vcf
sample_to_replace:
default: 'TUMOR'
new_sample_name: immuno_tumor_sample_name
out: [renamed_vcf]
rename_somatic_vcf_normal_sample:
run: ../tools/replace_vcf_sample_name.cwl
in:
input_vcf: rename_somatic_vcf_tumor_sample/renamed_vcf
sample_to_replace:
default: 'NORMAL'
new_sample_name: immuno_normal_sample_name
out: [renamed_vcf]
index_renamed_somatic:
run: ../tools/index_vcf.cwl
in:
vcf: rename_somatic_vcf_normal_sample/renamed_vcf
out:
[indexed_vcf]
phase_vcf:
run: ../subworkflows/phase_vcf.cwl
in:
somatic_vcf: index_renamed_somatic/indexed_vcf
germline_vcf: germline/final_vcf
reference: reference
reference_dict: reference_dict
bam: somatic/tumor_cram
normal_sample_name: immuno_normal_sample_name
tumor_sample_name: immuno_tumor_sample_name
out:
[phased_vcf]
extract_alleles:
run: ../tools/extract_hla_alleles.cwl
in:
allele_file: germline/optitype_tsv
out:
[allele_string]
pvacseq:
run: ../subworkflows/pvacseq.cwl
in:
detect_variants_vcf: index_renamed_somatic/indexed_vcf
sample_name: immuno_tumor_sample_name
normal_sample_name: immuno_normal_sample_name
rnaseq_bam: rnaseq/final_bam
reference_fasta: reference
readcount_minimum_base_quality: readcount_minimum_base_quality
readcount_minimum_mapping_quality: readcount_minimum_mapping_quality
gene_expression_file: rnaseq/gene_abundance
transcript_expression_file: rnaseq/transcript_abundance_tsv
alleles: extract_alleles/allele_string
prediction_algorithms: prediction_algorithms
epitope_lengths: epitope_lengths
binding_threshold: binding_threshold
allele_specific_binding_thresholds: allele_specific_binding_thresholds
minimum_fold_change: minimum_fold_change
peptide_sequence_length: peptide_sequence_length
top_score_metric: top_score_metric
additional_report_columns: additional_report_columns
fasta_size: fasta_size
downstream_sequence_length: downstream_sequence_length
exclude_nas: exclude_nas
phased_proximal_variants_vcf: phase_vcf/phased_vcf
maximum_transcript_support_level: maximum_transcript_support_level
normal_cov: normal_cov
tdna_cov: tdna_cov
trna_cov: trna_cov
normal_vaf: normal_vaf
tdna_vaf: tdna_vaf
trna_vaf: trna_vaf
expn_val: expn_val
net_chop_method: net_chop_method
net_chop_threshold: net_chop_threshold
netmhc_stab: netmhc_stab
n_threads: pvacseq_threads
variants_to_table_fields: variants_to_table_fields
variants_to_table_genotype_fields: variants_to_table_genotype_fields
vep_to_table_fields: vep_to_table_fields
out:
[annotated_vcf, annotated_tsv, mhc_i_all_epitopes, mhc_i_filtered_epitopes, mhc_i_ranked_epitopes, mhc_ii_all_epitopes, mhc_ii_filtered_epitopes, mhc_ii_ranked_epitopes, combined_all_epitopes, combined_filtered_epitopes, combined_ranked_epitopes]