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📚 update pubapp styling
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@dmiller15
dmiller15 committed May 23, 2024
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112 changes: 56 additions & 56 deletions workflows/kfdrc_tumor_only_dna_wf.cwl
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Expand Up @@ -104,87 +104,87 @@ inputs:
run_manta: {type: 'boolean?', default: true, doc: "Set to false to disable Manta"}
run_controlfreec: {type: 'boolean?', default: true, doc: "Set to false to disable Control-FREEC"}
run_calmd_bam: {type: 'boolean?', default: false, doc: "Set to true to enable samtools calmd running for BAM inputs"}
make_bamout: {type: 'boolean?', default: false, doc: "Should Mutect2 create a BAM output? Turning on this mode may result in serious\
\ performance cost for the caller."}
run_orientation_bias_mixture_model_filter: {type: 'boolean?', default: true, doc: "Should Orientation Bias Mixture Model Filter\
\ be applied to Mutect2 outputs?"}
i_flag: {type: ['null', {type: enum, name: i_flag, symbols: ["Y", "N"]}], doc: "Flag to intersect germline calls on padded regions.\
\ Use N if you want to skip this or have a WGS run"}
make_bamout: {type: 'boolean?', default: false, doc: "Should Mutect2 create a BAM output? Turning on this mode may result in serious
performance cost for the caller."}
run_orientation_bias_mixture_model_filter: {type: 'boolean?', default: true, doc: "Should Orientation Bias Mixture Model Filter
be applied to Mutect2 outputs?"}
i_flag: {type: ['null', {type: enum, name: i_flag, symbols: ["Y", "N"]}], doc: "Flag to intersect germline calls on padded regions.
Use N if you want to skip this or have a WGS run"}
disable_hotspot_annotation: {type: 'boolean?', default: false, doc: "Set to true to disable Hotspot Annotation"}

# Shared
indexed_reference_fasta: {type: 'File', secondaryFiles: [{pattern: ".fai", required: true}, {pattern: "^.dict", required: true}],
doc: "Reference fasta to which the input reads were aligned. Must include FAI and DICT indicies", "sbg:suggestedValue": {class: File,
path: 60639014357c3a53540ca7a3, name: Homo_sapiens_assembly38.fasta, secondaryFiles: [{class: File, path: 60639016357c3a53540ca7af,
name: Homo_sapiens_assembly38.fasta.fai}, {class: File, path: 60639019357c3a53540ca7e7, name: Homo_sapiens_assembly38.dict}]}}
calling_regions: {type: 'File', doc: "BED or INTERVALLIST file containing a set of genomic regions over which the callers will be\
\ run. For WGS, this should be the wgs_calling_regions.interval_list. For WXS, the user must provide the appropriate regions\
\ for their analysis."}
blacklist_regions: {type: 'File?', doc: "BED or INTERVALLIST file containing a set of genomic regions to remove from the calling\
\ regions for SNV and SV calling."}
cnv_blacklist_regions: {type: 'File?', doc: "BED or INTERVALLIST file containing a set of genomic regions to remove from the calling\
\ regions for CNV calling only!", "sbg:suggestedValue": {class: File, path: 663d2bcc27374715fccd8c6d, name: somatic-hg38_CNV_and_centromere_blacklist.hg38liftover.list}}
calling_regions: {type: 'File', doc: "BED or INTERVALLIST file containing a set of genomic regions over which the callers will be
run. For WGS, this should be the wgs_calling_regions.interval_list. For WXS, the user must provide the appropriate regions for
their analysis."}
blacklist_regions: {type: 'File?', doc: "BED or INTERVALLIST file containing a set of genomic regions to remove from the calling
regions for SNV and SV calling."}
cnv_blacklist_regions: {type: 'File?', doc: "BED or INTERVALLIST file containing a set of genomic regions to remove from the calling
regions for CNV calling only!", "sbg:suggestedValue": {class: File, path: 663d2bcc27374715fccd8c6d, name: somatic-hg38_CNV_and_centromere_blacklist.hg38liftover.list}}
input_tumor_aligned: {type: 'File', secondaryFiles: [{pattern: ".bai", required: false}, {pattern: "^.bai", required: false}, {
pattern: ".crai", required: false}, {pattern: "^.crai", required: false}], doc: "BAM/SAM/CRAM file containing tumor reads",
"sbg:fileTypes": "BAM, CRAM, SAM"}
input_tumor_name: {type: 'string', doc: "BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument."}
old_tumor_name: {type: 'string?', doc: "If `SM:` sample name in the align file is different than `input_tumor_name`, you **must**\
\ provide it here"}
old_tumor_name: {type: 'string?', doc: "If `SM:` sample name in the align file is different than `input_tumor_name`, you **must**
provide it here"}
output_basename: {type: 'string', doc: "String value to use as basename for outputs"}
panel_of_normals: {type: 'File?', secondaryFiles: ['.tbi'], doc: "VCF file (and index) of sites observed in normal. A panel of normals\
\ can be a useful (optional) input to help filter out commonly seen sequencing noise that may appear as low allele-fraction\
\ somatic variants.", "sbg:fileTypes": "VCF, VCF.GZ"}
mutect2_af_only_gnomad_vcf: {type: 'File', secondaryFiles: ['.tbi'], doc: "Population vcf (and index) of germline sequencing containing\
\ allele fractions in VCF format.", "sbg:suggestedValue": {class: File, path: 5f50018fe4b054958bc8d2e3, name: af-only-gnomad.hg38.vcf.gz,
secondaryFiles: [{class: File, path: 5f50018fe4b054958bc8d2e5, name: af-only-gnomad.hg38.vcf.gz.tbi}]}, "sbg:fileTypes": "VCF,\
\ VCF.GZ"}
mutect2_alleles_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "VCF file (and index) containing set of alleles for which to\
\ force genotyping regardless of evidence", "sbg:fileTypes": "VCF, VCF.GZ"}
mutect2_exac_common_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "Exac Common VCF (and index) used for calculating contamination\
\ values used in filtering the Mutect VCF. If do not wish to perfom this filtering, remove this input.", "sbg:suggestedValue": {
panel_of_normals: {type: 'File?', secondaryFiles: ['.tbi'], doc: "VCF file (and index) of sites observed in normal. A panel of normals
can be a useful (optional) input to help filter out commonly seen sequencing noise that may appear as low allele-fraction somatic
variants.", "sbg:fileTypes": "VCF, VCF.GZ"}
mutect2_af_only_gnomad_vcf: {type: 'File', secondaryFiles: ['.tbi'], doc: "Population vcf (and index) of germline sequencing containing
allele fractions in VCF format.", "sbg:suggestedValue": {class: File, path: 5f50018fe4b054958bc8d2e3, name: af-only-gnomad.hg38.vcf.gz,
secondaryFiles: [{class: File, path: 5f50018fe4b054958bc8d2e5, name: af-only-gnomad.hg38.vcf.gz.tbi}]}, "sbg:fileTypes": "VCF,
VCF.GZ"}
mutect2_alleles_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "VCF file (and index) containing set of alleles for which to
force genotyping regardless of evidence", "sbg:fileTypes": "VCF, VCF.GZ"}
mutect2_exac_common_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "Exac Common VCF (and index) used for calculating contamination
values used in filtering the Mutect VCF. If do not wish to perfom this filtering, remove this input.", "sbg:suggestedValue": {
class: File, path: 5f500135e4b0370371c051ad, name: small_exac_common_3.hg38.vcf.gz, secondaryFiles: [{class: File, path: 5f500135e4b0370371c051af,
name: small_exac_common_3.hg38.vcf.gz.tbi}]}, "sbg:fileTypes": "VCF, VCF.GZ"}
bwa_mem_index_image: {type: 'File?', doc: "BWA-mem index image used for FilterAlignmentArtifacts. WARNING!!! Experimental Software!!!\
\ Do not provide unless you are absolutely certain you want to run FilterAlignmentArtifacts.", "sbg:fileTypes": "IMG"}
bwa_mem_index_image: {type: 'File?', doc: "BWA-mem index image used for FilterAlignmentArtifacts. WARNING!!! Experimental Software!!!
Do not provide unless you are absolutely certain you want to run FilterAlignmentArtifacts.", "sbg:fileTypes": "IMG"}
mutect2_extra_args: {type: 'string?', doc: "Any additional arguments for Mutect2. See GATK documentation for all available options."}
filtermutectcalls_extra_args: {type: 'string?', default: "--min-allele-fraction 0.01", doc: "Any additional arguments for FilterMutectCalls.\
\ See GATK documentation for all available options."}
select_vars_mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], default: "gatk", doc: "Choose\
\ 'gatk' for SelectVariants tool, or 'grep' for grep expression"}
filtermutectcalls_extra_args: {type: 'string?', default: "--min-allele-fraction 0.01", doc: "Any additional arguments for FilterMutectCalls.
See GATK documentation for all available options."}
select_vars_mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], default: "gatk", doc: "Choose
'gatk' for SelectVariants tool, or 'grep' for grep expression"}
mate_copynumber_file_sample: {type: 'File?', doc: "Tumor cpn file from previous run. If used, will override bam use"}
gem_mappability_file: {type: 'File?', doc: "GEM mappability file to make read count adjustments with"}
min_subclone_presence: {type: 'int?', doc: "Tool default 100 (meaning \"do not look for subclones\"). Suggested: 20 (or 0.2) for\
\ WGS and 30 (or 0.3) for WES."}
min_subclone_presence: {type: 'int?', doc: "Tool default 100 (meaning \"do not look for subclones\"). Suggested: 20 (or 0.2) for
WGS and 30 (or 0.3) for WES."}
cfree_ploidy: {type: 'int[]', doc: "Array of ploidy possibilities for ControlFreeC to try"}
cfree_mate_orientation_sample: {type: ['null', {type: enum, name: mate_orientation_sample, symbols: ["0", "FR", "RF", "FF"]}], default: "FR",
doc: "0 (for single ends), RF (Illumina mate-pairs), FR (Illumina paired-ends), FF (SOLiD mate-pairs)"}
b_allele: {type: 'File?', secondaryFiles: [{pattern: ".tbi", required: true}], doc: "germline calls, needed for BAF. GATK HC VQSR\
\ input recommended. Tool will prefilter for germline and pass if expression given", "sbg:suggestedValue": {class: File, path: 663e7c69f180a9177dd4212b,
b_allele: {type: 'File?', secondaryFiles: [{pattern: ".tbi", required: true}], doc: "germline calls, needed for BAF. GATK HC VQSR
input recommended. Tool will prefilter for germline and pass if expression given", "sbg:suggestedValue": {class: File, path: 663e7c69f180a9177dd4212b,
name: dbSNP_v153_ucsc-compatible.converted.vt.decomp.norm.common_snps.vcf.gz, secondaryFiles: [{class: File, path: 6509b6a37f6417197fc158fc,
name: dbSNP_v153_ucsc-compatible.converted.vt.decomp.norm.common_snps.vcf.gz.tbi}]}}
cfree_coeff_var: {type: 'float?', default: 0.05, doc: "Coefficient of variation to set window size. Default 0.05 recommended"}
cfree_sex: {type: ['null', {type: enum, name: sex, symbols: ["XX", "XY"]}], doc: "If known, XX for female, XY for male"}
# Annotation
annotsv_annotations_dir_tgz: {type: 'File?', doc: "TAR.GZ'd Directory containing annotations for AnnotSV", "sbg:fileTypes": "TAR,\
\ TAR.GZ, TGZ", "sbg:suggestedValue": {class: File, path: 6328ab26d01163633dabcc2e, name: annotsv_311_plus_ens105_annotations_dir.tgz}}
annotsv_annotations_dir_tgz: {type: 'File?', doc: "TAR.GZ'd Directory containing annotations for AnnotSV", "sbg:fileTypes": "TAR,
TAR.GZ, TGZ", "sbg:suggestedValue": {class: File, path: 6328ab26d01163633dabcc2e, name: annotsv_311_plus_ens105_annotations_dir.tgz}}
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}}
vep_buffer_size: {type: 'int?', default: 5000, doc: "Increase or decrease to balance speed and memory usage"}
dbnsfp: {type: 'File?', secondaryFiles: [.tbi, ^.readme.txt], doc: "VEP-formatted plugin file, index, and readme file containing\
\ dbNSFP annotations"}
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. Use ALL to grab all"}
merged: {type: 'boolean?', default: true, doc: "Set to true if merged cache used"}
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"}
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}]}
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}]}
mutect2_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,QSI,HotSpotAllele"}
mutect2_retain_fmt: {type: 'string?', doc: "csv string with FORMAT fields that you want to keep"}
mutect2_retain_ann: {type: 'string?', doc: "csv string of annotations (within the VEP CSQ/ANN) to retain as extra columns in MAF",
Expand All @@ -195,8 +195,8 @@ inputs:
name: gnomad.v3.1.1.custom.echtvar.zip}]}
gatk_filter_name: {type: 'string[]', doc: "Array of names for each filter tag to add, recommend: [\"GNOMAD_AF_HIGH\", \"AF_LOW\"\
, \"AD_LOW\""}
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: \"gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER == 'PASS'\", \"FORMAT/AF < 0.01\", \"\
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: \"gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER == 'PASS'\", \"FORMAT/AF < 0.01\", \"
FORMAT/AD[:1] < 1\"]"}
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,
Expand All @@ -212,18 +212,18 @@ inputs:
filtermutectcalls_memory: {type: 'int?', doc: "GB of memory to allocate to GATK FilterMutectCalls (hard-capped)"}
filteralignmentartifacts_cores: {type: 'int?', doc: "CPUs to allocate to GATK FilterAlignmentArtifacts"}
filteralignmentartifacts_memory: {type: 'int?', doc: "GB of memory to allocate to GATK FilterAlignmentArtifacts (hard-capped)"}
cfree_threads: {type: 'int?', default: 16, doc: "For ControlFreeC. Recommend 16 max, as I/O gets saturated after that losing any\
\ advantage"}
cfree_threads: {type: 'int?', default: 16, doc: "For ControlFreeC. Recommend 16 max, as I/O gets saturated after that losing any
advantage"}
manta_memory: {type: 'int?', doc: "GB of memory to allocate to Manta; defaults to 10 (soft-capped)"}
manta_cores: {type: 'int?', doc: "Number of cores to allocate to Manta; defaults to 18"}
outputs:
# Mutect2
mutect2_protected_outputs: {type: 'File[]?', outputSource: mutect2/mutect2_protected_outputs, doc: "VCF with SNV, MNV, and INDEL\
\ variant calls and of pipeline soft FILTER-added values in MAF and VCF format with annotation, VCF index, and MAF format output"}
mutect2_public_outputs: {type: 'File[]?', outputSource: mutect2/mutect2_public_outputs, doc: "Protected outputs, except MAF and\
\ VCF have had entries with soft FILTER values removed"}
mutect2_bam: {type: 'File?', outputSource: mutect2/mutect2_bam, doc: "BAM generated by Mutect2, if desired. The assembled haplotypes\
\ and locally realigned reads will be written as BAM. Really for debugging purposes only."}
mutect2_protected_outputs: {type: 'File[]?', outputSource: mutect2/mutect2_protected_outputs, doc: "VCF with SNV, MNV, and INDEL
variant calls and of pipeline soft FILTER-added values in MAF and VCF format with annotation, VCF index, and MAF format output"}
mutect2_public_outputs: {type: 'File[]?', outputSource: mutect2/mutect2_public_outputs, doc: "Protected outputs, except MAF and
VCF have had entries with soft FILTER values removed"}
mutect2_bam: {type: 'File?', outputSource: mutect2/mutect2_bam, doc: "BAM generated by Mutect2, if desired. The assembled haplotypes
and locally realigned reads will be written as BAM. Really for debugging purposes only."}
ctrlfreec_pval: {type: 'File?', outputSource: controlfreec/ctrlfreec_pval, doc: 'Copy number call with GT (if BAF provided) and
p values. Most people want this'}
ctrlfreec_config: {type: 'File?', outputSource: controlfreec/ctrlfreec_config, doc: 'Config file used to run'}
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