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call_variants.cwl
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call_variants.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
SchemaDefRequirement:
types:
- $import: ../../resources/schemas/variants_tools.yaml
- $import: ../../resources/schemas/params/mutect.yaml
- $import: ../../resources/schemas/params/vardict.yaml
inputs:
run_tools: ../../resources/schemas/variants_tools.yaml#run_tools
mutect_params: ../../resources/schemas/params/mutect.yaml#mutect_params
vardict_params: ../../resources/schemas/params/vardict.yaml#vardict_params
tumor_bam:
type: File
secondaryFiles: [^.bai]
normal_bam:
type: File
secondaryFiles: [^.bai]
tumor_sample_name: string
normal_sample_name: string
dbsnp:
type: File
secondaryFiles: [.idx]
cosmic:
type: File
secondaryFiles: [.idx]
bed_file: File
reference_fasta: File
outputs:
mutect_vcf:
type: File
outputSource: mutect/output
mutect_callstats:
type: File
outputSource: mutect/callstats_output
vardict_vcf:
type: File
outputSource: vardict/output
steps:
vardict:
run: ../../cwl_tools/vardict/vardict_paired.cwl
in:
run_tools: run_tools
vardict:
valueFrom: $(inputs.run_tools.vardict)
testsomatic:
valueFrom: $(inputs.run_tools.vardict_testsomatic)
var2vcf_paired:
valueFrom: $(inputs.run_tools.vardict_var2vcf_paired)
vardict_params: vardict_params
reference_fasta: reference_fasta
bed_file: bed_file
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
column_for_region_end:
valueFrom: $(inputs.vardict_params.column_for_region_end)
column_for_region_start:
valueFrom: $(inputs.vardict_params.column_for_region_start)
column_for_chromosome:
valueFrom: $(inputs.vardict_params.column_for_chromosome)
column_for_gene_name:
valueFrom: $(inputs.vardict_params.column_for_gene_name)
allele_freq_thres:
valueFrom: $(inputs.vardict_params.allele_freq_thres)
min_num_variant_reads:
valueFrom: $(inputs.vardict_params.min_num_variant_reads)
output_file_name:
valueFrom: $(inputs.tumor_sample_name + '.' + inputs.normal_sample_name + '.vardict.vcf')
out: [output]
mutect:
run: ../../cwl_tools/mutect/mutect.cwl
in:
run_tools: run_tools
java_7:
valueFrom: $(inputs.run_tools.java_7)
mutect:
valueFrom: $(inputs.run_tools.mutect)
mutect_params: mutect_params
reference_sequence: reference_fasta
dbsnp: dbsnp
cosmic: cosmic
intervals: bed_file
input_file_normal: normal_bam
input_file_tumor: tumor_bam
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
read_filter:
valueFrom: $(inputs.mutect_params.read_filter)
downsample_to_coverage:
valueFrom: $(inputs.mutect_params.dcov)
fraction_contamination:
valueFrom: $(inputs.mutect_params.fraction_contamination)
minimum_mutation_cell_fraction:
valueFrom: $(inputs.mutect_params.minimum_mutation_cell_fraction)
vcf:
valueFrom: $(inputs.tumor_sample_name + '.' + inputs.normal_sample_name + '.mutect.vcf')
out:
valueFrom: $(inputs.tumor_sample_name + '.' + inputs.normal_sample_name + '.mutect.txt')
out: [output, callstats_output]