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p✏️ minor cwl doc cleanup and doc cleanup #186

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May 21, 2024
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p✏️ minor cwl doc cleanup and doc cleanup #186

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eb3e523
:pencil: minor cwl doc cleanup and doc cleanup
migbro May 21, 2024
18f13c8
update docker table
migbro May 21, 2024
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2 changes: 1 addition & 1 deletion docs/dockers_consensus.md
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Expand Up @@ -3,7 +3,7 @@
TOOL|DOCKER
-|-
add_strelka2_fields.cwl|pgc-images.sbgenomics.com/d3b-bixu/add-strelka2-fields:1.0.0
bcftools_filter_vcf.cwl|pgc-images.sbgenomics.com/d3b-bixu/bvcftools:latest
bcftools_filter_vcf.cwl|pgc-images.sbgenomics.com/d3b-bixu/bcftools:1.20
bcftools_strip_ann.cwl|pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest
consensus_merge.cwl|pgc-images.sbgenomics.com/d3b-bixu/consensus-merge:1.1.0
echtvar_anno.cwl|pgc-images.sbgenomics.com/d3b-bixu/echtvar:0.2.0
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2 changes: 1 addition & 1 deletion docs/dockers_somatic.md
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Expand Up @@ -9,7 +9,7 @@ annotsv.cwl|pgc-images.sbgenomics.com/d3b-bixu/annotsv:3.1.1
awk_chrlen_builder.cwl|ubuntu:22.04
awk_min_seg_length.cwl|ubuntu:20.04
bcbio_filter_vardict_somatic.cwl|pgc-images.sbgenomics.com/d3b-bixu/bcbio_vardict_filter
bcftools_filter_vcf.cwl|pgc-images.sbgenomics.com/d3b-bixu/bvcftools:latest
bcftools_filter_vcf.cwl|pgc-images.sbgenomics.com/d3b-bixu/bcftools:1.20
bcftools_reheader_samples_index.cwl|staphb/bcftools:1.17
bcftools_strip_ann.cwl|pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest
bedtools_intersect.cwl|pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest
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4 changes: 2 additions & 2 deletions docs/kfdrc-consensus-calling.md
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Expand Up @@ -48,12 +48,12 @@ The general outline is as follows:
- tool_name: "consensus_somatic"
- ncallers: # Optional number of callers required for consensus, recommend `2`
- consensus_ram: `3`
- annotation_zip: gnomad_3_1_1.vwb_subset.echtvar_0_1_9.zip # population stats VCF for public filtering
- annotation_zip: gnomad.v3.1.1.custom.echtvar.zip # population stats VCF for public filtering
- vep_cache: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz
- gatk_filter_name: `[NORM_DP_LOW, GNOMAD_AF_HIGH]`
- gatk_filter_expression: `[ vc.getGenotype('`_insert_norm_sample_id_here_`').getDP() <= 7,gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS']`
- bcftools_public_filter: `FILTER="PASS"|INFO/HotSpotAllele=1`
- retain_info: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele
- retain_info: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele"
- retain_fmt: # csv string with FORMAT fields that you want to keep
- retain_ann: "HGVSg"
- maf_center: "."
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104 changes: 40 additions & 64 deletions workflow/kfdrc_consensus_calling.cwl
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Expand Up @@ -24,7 +24,7 @@ doc: |
- `AD`, `DP`, and `AF` are calculated as the average value between callers
- `ADR`, `DPR`, and `AFR` fields are added as the range of values from the previous point, to give the observer a sense on confidence in the value
1. VEP Annotate Consensus (see [Kids First DRC Somatic Variant Annotation Workflow](https://github.com/kids-first/kf-somatic-workflow/blob/master/docs/kfdrc_annotation_wf.md) for details )
1. BCF tools annotate
1. Echtvar Annotation
- Additional annotation is performed augment VEP annotation
- While VEP does have extensive gnomad allele frequency annotation, it is limited to exome values. The added gnomad AF only resource we use augments this as an additional `INFO/AF` field to add WGS frequencies
1. Soft filter variants
Expand Down Expand Up @@ -53,11 +53,10 @@ doc: |
- tool_name: "consensus_somatic"
- ncallers: # Optional number of callers required for consensus, recommend `2`
- consensus_ram: `3`
- annotation_vcf: gnomad_3.1.1.vwb_subset.vcf.gz # population stats VCF for public filtering
- annotation_zip: gnomad.v3.1.1.custom.echtvar.zip # population stats VCF for public filtering
- vep_cache: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz
- annot_columns: "INFO/gnomad_3_1_1_AC:=INFO/AC,INFO/gnomad_3_1_1_AN:=INFO/AN,INFO/gnomad_3_1_1_AF:=INFO/AF,INFO/gnomad_3_1_1_nhomalt:=INFO/nhomalt,INFO/gnomad_3_1_1_AC_popmax:=INFO/AC_popmax,INFO/gnomad_3_1_1_AN_popmax:=INFO/AN_popmax,INFO/gnomad_3_1_1_AF_popmax:=INFO/AF_popmax,INFO/gnomad_3_1_1_nhomalt_popmax:=INFO/nhomalt_popmax,INFO/gnomad_3_1_1_AC_controls_and_biobanks:=INFO/AC_controls_and_biobanks,INFO/gnomad_3_1_1_AN_controls_and_biobanks:=INFO/AN_controls_and_biobanks,INFO/gnomad_3_1_1_AF_controls_and_biobanks:=INFO/AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer:=INFO/AF_non_cancer,INFO/gnomad_3_1_1_primate_ai_score:=INFO/primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence:=INFO/splice_ai_consequence"
- gatk_filter_name: `[NORM_DP_LOW, GNOMAD_AF_HIGH]`
- gatk_filter_expression: `[ vc.getGenotype('`_insert_norm_sample_id_here_`').getDP() <= 7,gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS' ]`
- gatk_filter_expression: `[ vc.getGenotype('`_insert_norm_sample_id_here_`').getDP() <= 7,gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS']`
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why not both?

Suggested change
- gatk_filter_expression: `[ vc.getGenotype('`_insert_norm_sample_id_here_`').getDP() <= 7,gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS']`
- gatk_filter_expression: `[vc.getGenotype('`_insert_norm_sample_id_here_`').getDP() <= 7,gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS']`

- bcftools_public_filter: `FILTER="PASS"|INFO/HotSpotAllele=1`
- retain_info: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele"
- retain_fmt: # csv string with FORMAT fields that you want to keep
Expand All @@ -77,80 +76,57 @@ requirements:
- class: InlineJavascriptRequirement

inputs:
indexed_reference_fasta: {type: 'File', secondaryFiles: ['.fai', '^.dict'], "sbg:suggestedValue": {
class: File, path: 60639014357c3a53540ca7a3, name: Homo_sapiens_assembly38.fasta,
secondaryFiles: [{class: File, path: 60639016357c3a53540ca7af, name: Homo_sapiens_assembly38.fasta},
indexed_reference_fasta: {type: 'File', secondaryFiles: ['.fai', '^.dict'], "sbg:suggestedValue": {class: File, path: 60639014357c3a53540ca7a3,
name: Homo_sapiens_assembly38.fasta, secondaryFiles: [{class: File, path: 60639016357c3a53540ca7af, name: Homo_sapiens_assembly38.fasta},
{class: File, path: 60639019357c3a53540ca7e7, name: Homo_sapiens_assembly38.dict}]}}
strelka2_vcf: {type: 'File', secondaryFiles: ['.tbi']}
mutect2_vcf: {type: 'File', secondaryFiles: ['.tbi']}
lancet_vcf: {type: 'File', secondaryFiles: ['.tbi']}
vardict_vcf: {type: 'File', secondaryFiles: ['.tbi']}
cram: {type: 'File', secondaryFiles: ['.crai'], doc: "Tumor cram recommended for\
\ MQ score calculation"}
cram: {type: 'File', secondaryFiles: ['.crai'], doc: "Tumor cram recommended for MQ score calculation"}
input_tumor_name: string
input_normal_name: string
output_basename: string
tool_name: {type: 'string?', default: "consensus_somatic", doc: "A helpful file\
\ name building component"}
ncallers: {type: 'int?', doc: "Optional number of callers required for consensus\
\ [2]", default: 2}
hotspot_source: {type: 'string?', doc: "Optional description of hotspot definition\
\ source"}
contig_bed: {type: 'File?', doc: "Optional BED file containing names of target contigs\
\ / chromosomes"}
consensus_ram: {type: 'int?', doc: "Set min memory in GB for consensus merge step",
default: 3}
vep_cache: {type: 'File', doc: "tar gzipped cache from ensembl/local converted cache",
"sbg:suggestedValue": {class: File, path: 6332f8e47535110eb79c794f, name: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz}}
dbnsfp: {type: 'File?', secondaryFiles: [.tbi, ^.readme.txt], doc: "VEP-formatted\
\ plugin file, index, and readme file containing dbNSFP annotations"}
dbnsfp_fields: {type: 'string?', doc: "csv string with desired fields to annotate\
\ if dbnsfp provided. Use ALL to grab all"}
tool_name: {type: 'string?', default: "consensus_somatic", doc: "A helpful file name building component"}
ncallers: {type: 'int?', doc: "Optional number of callers required for consensus [2]", default: 2}
hotspot_source: {type: 'string?', doc: "Optional description of hotspot definition source"}
contig_bed: {type: 'File?', doc: "Optional BED file containing names of target contigs / chromosomes"}
consensus_ram: {type: 'int?', doc: "Set min memory in GB for consensus merge step", default: 3}
vep_cache: {type: 'File', doc: "tar gzipped cache from ensembl/local converted cache", "sbg:suggestedValue": {class: File, path: 6332f8e47535110eb79c794f,
name: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz}}
dbnsfp: {type: 'File?', secondaryFiles: [.tbi, ^.readme.txt], doc: "VEP-formatted plugin file, index, and readme file containing
dbNSFP annotations"}
dbnsfp_fields: {type: 'string?', doc: "csv string with desired fields to annotate if dbnsfp provided. Use ALL to grab all"}
merged: {type: 'boolean?', doc: "Set to true if merged cache used", default: true}
cadd_indels: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin\
\ file and index containing CADD indel annotations"}
cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file\
\ and index containing CADD SNV annotations"}
cadd_indels: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD indel annotations"}
cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD SNV annotations"}
run_cache_existing: {type: 'boolean?', doc: "Run the check_existing flag for cache"}
run_cache_af: {type: 'boolean?', doc: "Run the allele frequency flags for cache"}

# annotation vars
genomic_hotspots: {type: 'File[]?', doc: "Tab-delimited BED formatted file(s) containing\
\ hg38 genomic positions corresponding to hotspots", "sbg:suggestedValue": [
{class: File, path: 607713829360f10e3982a423, name: tert.bed}]}
protein_snv_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited\
\ file(s) containing protein names and amino acid positions corresponding to\
\ hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6a,
name: protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv}]}
protein_indel_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited\
\ file(s) containing protein names and amino acid position ranges corresponding\
\ to hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6f,
name: protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv}]}
retain_info: {type: 'string?', doc: "csv string with INFO fields that you want to\
\ keep", default: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele"}
retain_fmt: {type: 'string?', doc: "csv string with FORMAT fields that you want\
\ to keep"}
retain_ann: {type: 'string?', doc: "csv string of annotations (within the VEP CSQ/ANN)\
\ to retain as extra columns in MAF", default: "HGVSg"}
add_common_fields: {type: 'boolean?', doc: "Set to true if input is a strelka2 vcf\
\ that hasn't had common fields added", default: false}
bcftools_strip_columns: {type: 'string?', doc: "csv string of columns to strip if\
\ needed to avoid conflict, i.e INFO/AF"}
echtvar_anno_zips: {type: 'File[]?', doc: "Annotation ZIP files for echtvar anno",
"sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6, name: gnomad.v3.1.1.custom.echtvar.zip}]}
bcftools_public_filter: {type: 'string?', doc: "Will hard filter final result to
create a public version", default: FILTER="PASS"|INFO/HotSpotAllele=1}
gatk_filter_name: {type: 'string[]', doc: "Array of names for each filter tag to\
\ add, recommend: [\"NORM_DP_LOW\", \"GNOMAD_AF_HIGH\"]"}
gatk_filter_expression: {type: 'string[]', doc: "Array of filter expressions to\
\ establish criteria to tag variants with. See https://gatk.broadinstitute.org/hc/en-us/articles/360036730071-VariantFiltration,\
\ recommend: \"vc.getGenotype('\" + inputs.input_normal_name + \"').getDP()\
\ <= 7\"), \"gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && && gnomad_3_1_1_FILTER=='PASS'\"]"}
disable_hotspot_annotation: {type: 'boolean?', doc: "Disable Hotspot Annotation\
\ and skip this task.", default: true}
genomic_hotspots: {type: 'File[]?', doc: "Tab-delimited BED formatted file(s) containing hg38 genomic positions corresponding to
hotspots", "sbg:suggestedValue": [{class: File, path: 607713829360f10e3982a423, name: tert.bed}]}
protein_snv_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited file(s) containing protein names and amino acid
positions corresponding to hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6a, name: protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv}]}
protein_indel_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited file(s) containing protein names and amino
acid position ranges corresponding to hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6f, name: protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv}]}
retain_info: {type: 'string?', doc: "csv string with INFO fields that you want to keep", default: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele"}
retain_fmt: {type: 'string?', doc: "csv string with FORMAT fields that you want to keep"}
retain_ann: {type: 'string?', doc: "csv string of annotations (within the VEP CSQ/ANN) to retain as extra columns in MAF", default: "HGVSg"}
add_common_fields: {type: 'boolean?', doc: "Set to true if input is a strelka2 vcf that hasn't had common fields added", default: false}
bcftools_strip_columns: {type: 'string?', doc: "csv string of columns to strip if needed to avoid conflict, i.e INFO/AF"}
echtvar_anno_zips: {type: 'File[]?', doc: "Annotation ZIP files for echtvar anno", "sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6,
name: gnomad.v3.1.1.custom.echtvar.zip}]}
bcftools_public_filter: {type: 'string?', doc: "Will hard filter final result to create a public version", default: FILTER="PASS"|INFO/HotSpotAllele=1}
gatk_filter_name: {type: 'string[]', doc: "Array of names for each filter tag to add, recommend: [\"NORM_DP_LOW\", \"GNOMAD_AF_HIGH\"\
]"}
gatk_filter_expression: {type: 'string[]', doc: "Array of filter expressions to establish criteria to tag variants with. See https://gatk.broadinstitute.org/hc/en-us/articles/360036730071-VariantFiltration,
recommend: \"vc.getGenotype('\" + inputs.input_normal_name + \"').getDP() <= 7\"), \"gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF
> 0.001 && && gnomad_3_1_1_FILTER=='PASS'\"]"}
disable_hotspot_annotation: {type: 'boolean?', doc: "Disable Hotspot Annotation and skip this task.", default: true}
maf_center: {type: 'string?', doc: "Sequencing center of variant called", default: "."}
custom_enst: { type: 'File?', doc: "Use a file with ens tx IDs for each gene to override VEP PICK", "sbg:suggestedValue": {class: File, path: 663d2bcc27374715fccd8c65,
name: kf_isoform_override.tsv} }
custom_enst: {type: 'File?', doc: "Use a file with ens tx IDs for each gene to override VEP PICK", "sbg:suggestedValue": {class: File,
path: 663d2bcc27374715fccd8c65, name: kf_isoform_override.tsv}}

outputs:
annotated_protected_outputs: {type: 'File[]', outputSource: annotate/annotated_protected}
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