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schema.yaml
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---
algorithm:
type: 'List'
required: true
help: 'List of sSNV algorithms'
default:
- mutect2
- somaticsniper
- strelka2
- muse
choices:
- mutect2
- somaticsniper
- strelka2
- muse
reference:
type: 'Path'
mode: 'r'
required: true
help: 'Absolute path to reference directory'
intersect_regions:
type: 'Path'
required: true
help: 'call regions bed file used by mutect2, strelka2 and intersect'
output_dir:
type: 'Path'
mode: 'w'
required: true
help: 'Absolute path to output directory'
work_dir:
type: 'Path'
mode: 'w'
required: false
help: 'Absolute path to output directory'
dataset_id:
type: 'String'
required: true
help: 'Dataset identifier'
exome:
type: 'Bool'
required: false
default: false
help: 'The exome option when running manta and strelka2'
save_intermediate_files:
type: 'Bool'
required: false
default: false
help: 'The option to save the intermediate files'
bgzip_extra_args:
type: 'String'
required: false
allow_empty: true
default: ''
help: 'Additional arguments for bgzip command'
tabix_extra_args:
type: 'String'
required: false
allow_empty: true
default: ''
help: 'Additional arguments for tabix command'
split_intervals_extra_args:
type: 'String'
required: false
allow_empty: true
help: 'Additional arguments for the SplitIntervals command'
mutect2_extra_args:
type: 'String'
required: false
allow_empty: true
help: 'Additional arguments for the Mutect2 command'
filter_mutect_calls_extra_args:
type: 'String'
required: false
allow_empty: true
help: 'Additional arguments for the FilterMutectCalls command'
scatter_count:
type: 'Integer'
required: true
germline_resource_gnomad_vcf:
type: 'Path'
required: false
panel_of_normals_vcf:
type: 'Path'
required: false
help: 'VCF file of sites observed in a set of normal samples'
dbSNP:
type: 'Path'
required: true
ncbi_build:
type: 'String'
required: true
help: 'NCBI build version, e.g. GRCh38'
vcf2maf_extra_args:
type: 'String'
required: false
allow_empty: true
help: 'Additional arguments for the vcf2maf command'
patient_id:
type: 'String'
required: true
help: 'Patient identifier'
base_resource_update:
type: 'ResourceUpdateNamespace'
required: false
help: 'User-defined modifications for adjusting base resource allocations for processes'
elements:
memory:
type: 'ResourceUpdateList'
required: false
help: 'List of memory updates'
cpus:
type: 'ResourceUpdateList'
required: false
help: 'List of CPU updates'
input:
type: 'InputNamespace'
required: true
help: 'Input to process'
elements:
tumor:
type: 'BAMEntryList'
required: false
help: 'Tumor id/path input'
elements:
BAM:
type: 'Path'
mode: 'r'
required: true
help: 'Absolute path to tumor sample BAM files'
contamination_table:
type: 'Path'
mode: 'r'
required: false
help: 'Absolute path to contamination.tables'
normal:
type: 'BAMEntryList'
required: false
help: 'Normal id/path input'
elements:
BAM:
type: 'Path'
mode: 'r'
required: true
help: 'Absolute path to normal sample BAM files'
muse:
type: 'Path'
mode: 'r'
required: false
help: 'Absolute path to muse VCF file'
mutect2:
type: 'Path'
mode: 'r'
required: false
help: 'Absolute path to mutect2 VCF file'
somaticsniper:
type: 'Path'
mode: 'r'
required: false
help: 'Absolute path to somaticsniper VCF file'
strelka2:
type: 'Path'
mode: 'r'
required: false
help: 'Absolute path to strelka2 VCF file'