#/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
- $import: ../types/vep_custom_annotation.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?
#somatic inputs
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
label: "reference: Reference fasta file for a desired assembly"
doc: |
reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)
in fasta format for the entire genome. This is what reads will be aligned to.
Appropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html
When providing the reference secondary files corresponding to reference indices must be
located in the same directory as the reference itself. These files can be created with
samtools index, bwa index, and picard CreateSequenceDictionary.
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "tumor_sequence: MT sequencing data and readgroup information"
doc: |
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.
tumor_name:
type: string?
default: 'tumor'
label: "tumor_name: String specifying the name of the MT sample"
doc: |
tumor_name provides a string for what the MT sample will be referred to in the various
outputs, for example the VCF files.
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "normal_sequence: WT sequencing data and readgroup information"
doc: |
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.
normal_name:
type: string?
default: 'normal'
label: "normal_name: String specifying the name of the WT sample"
doc: |
normal_name provides a string for what the WT sample will be referred to in the various
outputs, for example the VCF files.
bqsr_known_sites:
type: File[]
secondaryFiles: [.tbi]
label: "bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis."
doc: |
Known polymorphic indels recommended by GATK for a variety of
tools including the BaseRecalibrator. This is part of the GATK resource
bundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213
File should be in vcf format, and tabix indexed.
bqsr_intervals:
type: string[]
label: "bqsr_intervals: Array of strings specifying regions for base quality score recalibration"
doc: |
bqsr_intervals provides an array of genomic intervals for which to apply
GATK base quality score recalibrations. Typically intervals are given
for the entire chromosome (chr1, chr2, etc.), these names should match
the format in the reference file.
bait_intervals:
type: File
label: "bait_intervals: interval_list file of baits used in the sequencing experiment"
doc: |
bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.
These are essentially coordinates for regions you were able to design probes for in the reagent.
Typically the reagent provider has this information available in bed format and it can be
converted to an interval_list with Picard BedToIntervalList. AstraZeneca also maintains a repo
of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data
target_intervals:
type: File
label: "target_intervals: interval_list file of targets used in the sequencing experiment"
doc: |
target_intervals is an interval_list corresponding to the targets for the capture reagent.
BED files with this information can be converted to interval_lists with Picard BedToIntervalList.
In general for a WES exome reagent bait_intervals and target_intervals are the same.
target_interval_padding:
type: int
label: "target_interval_padding: number of bp flanking each target region in which to allow variant calls"
doc: |
The effective coverage of capture products generally extends out beyond the actual regions
targeted. This parameter allows variants to be called in these wingspan regions, extending
this many base pairs from each side of the target regions.
default: 100
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
strelka_cpu_reserved:
type: int?
default: 8
scatter_count:
type: int
doc: "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs"
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]
doc: "Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)"
filter_docm_variants:
type: boolean?
default: true
doc: "Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls"
vep_cache_dir:
type:
- string
- Directory
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]
vep_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
manta_call_regions:
type: File?
secondaryFiles: [.tbi]
manta_non_wgs:
type: boolean?
default: true
manta_output_contigs:
type: boolean?
somalier_vcf:
type: File
validated_variants:
type: File?
secondaryFiles: [.tbi]
doc: "An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF"
#germline inputs
gvcf_gq_bands:
type: string[]
gatk_haplotypecaller_intervals:
type:
type: array
items:
type: array
items: string
ploidy:
type: int?
optitype_name:
type: string?
#phase_vcf inputs
reference_dict:
type: File
clinical_mhc_classI_alleles:
type: string[]?
label: "Clinical HLA typing results, limited to MHC Class I alleles; element format: HLA-X*01:02[/HLA-X...]"
doc: "used to provide clinical HLA typing results in the format HLA-X*01:02[/HLA-X...] when available."
clinical_mhc_classII_alleles:
type: string[]?
label: "Clinical HLA typing results, limited to MHC Class II alleles"
doc: "used to provide clinical HLA typing results; separated from class I due to nomenclature inconsistencies"
#pvacseq inputs
readcount_minimum_base_quality:
type: int?
readcount_minimum_mapping_quality:
type: int?
prediction_algorithms:
type: string[]
epitope_lengths_class_i:
type: int[]?
epitope_lengths_class_ii:
type: int[]?
binding_threshold:
type: int?
percentile_threshold:
type: int?
allele_specific_binding_thresholds:
type: boolean?
minimum_fold_change:
type: float?
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"]
label: "net_chop_method: NetChop prediction method to use ('cterm' for C term 3.0, '20s' for 20S 3.0)"
doc: |
net_chop_method is used to specify which NetChop prediction method to use ("cterm" for C term 3.0, "20s" for 20S 3.0).
C-term 3.0 is trained with publicly available MHC class I ligands and the authors believe that is performs best in predicting the
boundaries of CTL epitopes. 20S is trained with in vitro degradation data.
net_chop_threshold:
type: float?
label: "net_chop_threshold: NetChop prediction threshold"
doc: |
net_chop_threshold specifies the threshold to use for NetChop prediction; increasing the threshold results in better specificity, but worse sensitivity.
netmhc_stab:
type: boolean?
label: "netmhc_stab: sets an option whether to run NetMHCStabPan or not"
doc: |
netmhc_stab sets an option that decides whether it will run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes.
run_reference_proteome_similarity:
type: boolean?
label: "run_reference_proteome_similarity: sets an option whether to run reference proteome similarity or not"
doc: |
run_reference_proteome_similarity sets an option that decides whether it will run reference proteome similarity after all filtering and BLAST peptide sequences against the reference proteome to see if they appear elsewhere in the proteome.
pvacseq_threads:
type: int?
label: "pvacseq_threads: Number of threads to use for parallelizing pvacseq prediction"
doc: |
pvacseq_threads specifies the number of threads to use for parallelizing peptide-MHC binding prediction calls.
tumor_sample_name:
type: string
label: "tumor_sample_name: Name of the tumor sample"
doc: |
tumor_sample_name is the name of the tumor sample being processed. When processing a multi-sample VCF the sample name must be a sample ID in the input VCF #CHROM header line.
normal_sample_name:
type: string
label: "tumor_sample_name: Name of the normal sample"
doc: |
normal_sample_name is the name of the normal sample to use for phasing of germline variants.
outputs:
final_bigwig:
type: File
outputSource: rnaseq/bamcoverage_bigwig
final_bam:
type: File
outputSource: rnaseq/final_bam
secondaryFiles: [.bai]
label: "Sorted BAM from tumor RNA"
doc: |
Sorted BAM file of sequencing read alignments by HISAT2 with duplicate reads tagged
stringtie_transcript_gtf:
type: File
outputSource: rnaseq/stringtie_transcript_gtf
label: "Transcript GTF assembled from tumor RNA by StringTie"
doc: |
GTF file containing the transcripts assembled from the tumor RNA sample, created by StringTie
stringtie_gene_expression_tsv:
type: File
outputSource: rnaseq/stringtie_gene_expression_tsv
label: "Gene abundance table from tumor RNA by StringTie"
doc: |
Tab-delimited file containing gene abundances in FPKM and TPM, created by StringTie
transcript_abundance_tsv:
type: File
outputSource: rnaseq/transcript_abundance_tsv
label: "Transcript-level abundance table by kallisto"
doc: |
Tab-delimited file containing transcript-level abundance estimates in TPM, created by kallisto
transcript_abundance_h5:
type: File
outputSource: rnaseq/transcript_abundance_h5
label: "Transcript-level abundance table in HDF5 format by kallisto"
doc: |
HDF5 binary file containing transcript-level abundance esimates, bootstrap estimate, and so on, created by kallisto
gene_abundance:
type: File
outputSource: rnaseq/gene_abundance
label: "Gene-level abundance output by tximport with kallisto output"
doc: |
Tab-delimited file containing the abundance estimates summarized in the gene level with kallisto output by Bioconductor tximport tool
metrics:
type: File
outputSource: rnaseq/metrics
label: "RNA-seq Diagnosis/quality metrics from tumor RNA"
doc: |
RNA-seq Diagnosis/quality metrics showing the distribution of the bases within the transcripts, created by picard CollectRnaSeqMetrics tool
chart:
type: File?
outputSource: rnaseq/chart
label: "Plot for RNA-seq diagnosis/quality metrics"
doc: |
PDF file for the plot of RNA sequencing coverage at the normalized position across transcript as RNA-seq diagnosis/quality metrics, created by picard CollectRnaSeqMetrics tool
tumor_cram:
type: File
outputSource: somatic/tumor_cram
label: "Sorted CRAM from tumor DNA"
doc: |
Sorted CRAM file of sequencing read alignments by bwa-mem from a tumor DNA sample with duplicate reads tagged
tumor_mark_duplicates_metrics:
type: File
outputSource: somatic/tumor_mark_duplicates_metrics
label: "Sequencing duplicate metrics from tumor DNA"
doc: |
Duplication metrics on duplicate sequencing reads from a tumor DNA sample, identified by picard MarkDuplicates tool
tumor_insert_size_metrics:
type: File
outputSource: somatic/tumor_insert_size_metrics
label: "Paired-end sequencing diagnosis/quality metrics from tumor DNA"
doc: |
Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a tumor DNA sample
tumor_alignment_summary_metrics:
type: File
outputSource: somatic/tumor_alignment_summary_metrics
label: "Sequencign alignment summary from tumor DNA"
doc: |
Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a tumor DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool
tumor_hs_metrics:
type: File
outputSource: somatic/tumor_hs_metrics
label: "Sequencing coverage summary of target intervals from tumor DNA"
doc: |
Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a tumor DNA sample, for example to assess target coverage of WES
tumor_per_target_coverage_metrics:
type: File[]
outputSource: somatic/tumor_per_target_coverage_metrics
label: "Sequencing per-target coverage summary of target intervals from tumor DNA"
doc: |
Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample
tumor_per_target_hs_metrics:
type: File[]
outputSource: somatic/tumor_per_target_hs_metrics
label: "Sequencing coverage summary of target intervals from tumor DNA"
doc: |
Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample
tumor_per_base_coverage_metrics:
type: File[]
outputSource: somatic/tumor_per_base_coverage_metrics
label: "Sequencing per-base coverage summary at target sites from tumor DNA"
doc: |
Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample
tumor_per_base_hs_metrics:
type: File[]
outputSource: somatic/tumor_per_base_hs_metrics
label: "Sequencing coverage summary at target sites from tumor DNA"
doc: |
Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample
tumor_summary_hs_metrics:
type: File[]
outputSource: somatic/tumor_summary_hs_metrics
tumor_flagstats:
type: File
outputSource: somatic/tumor_flagstats
label: "Sequencing count metrics based on SAM FLAG field from tumor sample"
doc: |
Summary with the count numbers of alignments for each FLAG type from a tumor DNA sample, including 13 categories based on the bit flags in the FLAG field
tumor_verify_bam_id_metrics:
type: File
outputSource: somatic/tumor_verify_bam_id_metrics
label: "Sequencing quality assessment metric for tumor sample contamination"
doc: |
verifyBamID output files containing the contamination estimate in a tumor DNA sample, across all readGroups and per readGroup separately
tumor_verify_bam_id_depth:
type: File
outputSource: somatic/tumor_verify_bam_id_depth
label: "Sequencing quality assessment metric for tumor sample genotyping"
doc: |
verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a tumor DNA sample, across all readGroups and per readGroup separately
normal_cram:
type: File
outputSource: somatic/normal_cram
label: "Sorted CRAM from normal DNA"
doc: |
Sorted CRAM file of sequencing read alignments by bwa-mem from a normal DNA sample with duplicate reads tagged
normal_mark_duplicates_metrics:
type: File
outputSource: somatic/normal_mark_duplicates_metrics
label: "Sequencing duplicate metrics from normal DNA"
doc: |
Duplication metrics on duplicate sequencing reads from a normal DNA sample, identified by picard MarkDuplicates tool
normal_insert_size_metrics:
type: File
outputSource: somatic/normal_insert_size_metrics
label: "Paired-end sequencing diagnosis/quality metrics from normal DNA"
doc: |
Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a normal DNA sample
normal_alignment_summary_metrics:
type: File
outputSource: somatic/normal_alignment_summary_metrics
label: "Sequencign alignment summary from normal DNA"
doc: |
Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a normal DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool
normal_hs_metrics:
type: File
outputSource: somatic/normal_hs_metrics
label: "Sequencing coverage summary of target intervals from normal DNA"
doc: |
Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a normal DNA sample, for example to assess target coverage
normal_per_target_coverage_metrics:
type: File[]
outputSource: somatic/normal_per_target_coverage_metrics
label: "Sequencing per-target coverage summary of target intervals from normal DNA"
doc: |
Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample
normal_per_target_hs_metrics:
type: File[]
outputSource: somatic/normal_per_target_hs_metrics
label: "Sequencing coverage summary of target intervals from normal DNA"
doc: |
Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample
normal_per_base_coverage_metrics:
type: File[]
outputSource: somatic/normal_per_base_coverage_metrics
label: "Sequencing per-base coverage summary at target sites from normal DNA"
doc: |
Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample
normal_per_base_hs_metrics:
type: File[]
outputSource: somatic/normal_per_base_hs_metrics
label: "Sequencing coverage summary at target sites from normal DNA"
doc: |
Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample
normal_summary_hs_metrics:
type: File[]
outputSource: somatic/normal_summary_hs_metrics
normal_flagstats:
type: File
outputSource: somatic/normal_flagstats
label: "Sequencing count metrics based on SAM FLAG field from normal sample"
doc: |
Summary with the count numbers of alignments for each FLAG type from a normal DNA sample, including 13 categories based on the bit flags in the FLAG field
normal_verify_bam_id_metrics:
type: File
outputSource: somatic/normal_verify_bam_id_metrics
label: "Sequencing quality assessment metric for normal sample contamination"
doc: |
verifyBamID output files containing the contamination estimate in a normal DNA sample, across all readGroups and per readGroup separately
normal_verify_bam_id_depth:
type: File
outputSource: somatic/normal_verify_bam_id_depth
label: "Sequencing quality assessment metric for normal sample genotyping"
doc: |
verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a normal DNA sample, across all readGroups and per readGroup separately
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
germline_raw_vcf:
type: File
outputSource: germline/raw_vcf
secondaryFiles: [.tbi]
germline_final_vcf:
type: File
outputSource: germline/final_vcf
secondaryFiles: [.tbi]
germline_filtered_vcf:
type: File
outputSource: germline/filtered_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
consensus_alleles:
type: string[]
outputSource: hla_consensus/consensus_alleles
hla_call_files:
type: Directory
outputSource: hla_consensus/hla_call_files
annotated_vcf:
type: File
outputSource: pvacseq/annotated_vcf
annotated_tsv:
type: File
outputSource: pvacseq/annotated_tsv
pvacseq_predictions:
type: Directory
outputSource: pvacseq/pvacseq_predictions
steps:
rnaseq:
run: rnaseq.cwl
in:
reference: reference
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
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, bamcoverage_bigwig]
somatic:
run: somatic_exome.cwl
in:
reference: reference
tumor_sequence: tumor_sequence
tumor_name: tumor_name
normal_sequence: normal_sequence
normal_name: normal_name
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
target_interval_padding: target_interval_padding
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
strelka_cpu_reserved: strelka_cpu_reserved
scatter_count: 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
vep_custom_annotations: vep_custom_annotations
manta_call_regions: manta_call_regions
manta_non_wgs: manta_non_wgs
manta_output_contigs: manta_output_contigs
somalier_vcf: somalier_vcf
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
validated_variants: validated_variants
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
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
target_interval_padding: target_interval_padding
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
gvcf_gq_bands: gvcf_gq_bands
intervals: gatk_haplotypecaller_intervals
ploidy: ploidy
vep_cache_dir: vep_cache_dir
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
vep_custom_annotations: vep_custom_annotations
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
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,raw_vcf,final_vcf,filtered_vcf,vep_summary,optitype_tsv,optitype_plot]
phase_vcf:
run: ../subworkflows/phase_vcf.cwl
in:
somatic_vcf: somatic/final_filtered_vcf
germline_vcf: germline/final_vcf
reference: reference
reference_dict: reference_dict
bam: somatic/tumor_cram
normal_sample_name: normal_sample_name
tumor_sample_name: tumor_sample_name
out:
[phased_vcf]
extract_alleles:
run: ../tools/extract_hla_alleles.cwl
in:
allele_file: germline/optitype_tsv
out:
[allele_string]
hla_consensus:
run: ../tools/hla_consensus.cwl
in:
optitype_hla_alleles: extract_alleles/allele_string
clinical_mhc_classI_alleles: clinical_mhc_classI_alleles
clinical_mhc_classII_alleles: clinical_mhc_classII_alleles
out:
[consensus_alleles, hla_call_files]
intersect_passing_variants:
run: ../tools/intersect_known_variants.cwl
in:
vcf: somatic/final_filtered_vcf
validated_variants: validated_variants
out:
[validated_and_pipeline_vcf]
pvacseq:
run: ../subworkflows/pvacseq.cwl
in:
detect_variants_vcf: intersect_passing_variants/validated_and_pipeline_vcf
sample_name: tumor_sample_name
normal_sample_name: 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: hla_consensus/consensus_alleles
prediction_algorithms: prediction_algorithms
epitope_lengths_class_i: epitope_lengths_class_i
epitope_lengths_class_ii: epitope_lengths_class_ii
binding_threshold: binding_threshold
percentile_threshold: percentile_threshold
allele_specific_binding_thresholds: allele_specific_binding_thresholds
minimum_fold_change: minimum_fold_change
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
run_reference_proteome_similarity: run_reference_proteome_similarity
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, pvacseq_predictions]