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wgs_variant_calling_bam.cwl
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wgs_variant_calling_bam.cwl
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cwlVersion: v1.0
class: Workflow
id: wgs_variant_calling_bam
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
output_basename: string
sorted_bam:
type: File
secondaryFiles: ['.bai']
indexed_reference_fasta:
type: File
secondaryFiles: ['.64.amb', '.fai', '^.dict',
'.64.ann', '.64.bwt', '.64.pac', '.64.sa',
'.64.alt', '^.dict', '.amb', '.ann', '.bwt',
'.pac', '.sa']
dbsnp_vcf:
type: File
secondaryFiles: ['.idx']
knownsites: File[]
reference_dict: File
contamination_sites_bed: File
contamination_sites_mu: File
contamination_sites_ud: File
wgs_calling_interval_list: File
wgs_coverage_interval_list: File
wgs_evaluation_interval_list: File
genome: string
outputs:
gvcf: {type: File, outputSource: picard_mergevcfs/output}
verifybamid_output: {type: File, outputSource: verifybamid/output}
bqsr_report: {type: File, outputSource: gatk_gatherbqsrreports/output}
gvcf_calling_metrics: {type: 'File[]', outputSource: picard_collectgvcfcallingmetrics/output}
aggregation_metrics: {type: 'File[]', outputSource: picard_collectaggregationmetrics/output}
wgs_metrics: {type: File, outputSource: picard_collectwgsmetrics/output}
annotated_vcf: {type: File, outputSource: snpeff_g_vcf/outfile}
steps:
python_createsequencegroups:
run: ../tools/python_createsequencegroups.cwl
in:
ref_dict: reference_dict
out: [sequence_intervals]
gatk_baserecalibrator:
run: ../tools/gatk_baserecalibrator.cwl
in:
input_bam: sorted_bam
knownsites: knownsites
reference: indexed_reference_fasta
sequence_interval: python_createsequencegroups/sequence_intervals
scatter: [sequence_interval]
out: [output]
gatk_gatherbqsrreports:
run: ../tools/gatk_gatherbqsrreports.cwl
in:
input_brsq_reports: gatk_baserecalibrator/output
output_basename: output_basename
out: [output]
gatk_applybqsr:
run: ../tools/gatk_applybqsr.cwl
in:
bqsr_report: gatk_gatherbqsrreports/output
input_bam: sorted_bam
reference: indexed_reference_fasta
sequence_interval: python_createsequencegroups/sequence_intervals
scatter: [sequence_interval]
out: [recalibrated_bam]
picard_gatherbamfiles:
run: ../tools/picard_gatherbamfiles.cwl
in:
input_bam: gatk_applybqsr/recalibrated_bam
output_bam_basename: output_basename
out: [output]
picard_collectaggregationmetrics:
run: ../tools/picard_collectaggregationmetrics.cwl
in:
input_bam: picard_gatherbamfiles/output
reference: indexed_reference_fasta
out: [output]
picard_collectwgsmetrics:
run: ../tools/picard_collectwgsmetrics.cwl
in:
input_bam: picard_gatherbamfiles/output
intervals: wgs_coverage_interval_list
reference: indexed_reference_fasta
out: [output]
picard_intervallisttools:
run: ../tools/picard_intervallisttools.cwl
in:
interval_list: wgs_calling_interval_list
out: [output]
verifybamid:
run: ../tools/verifybamid.cwl
in:
contamination_sites_bed: contamination_sites_bed
contamination_sites_mu: contamination_sites_mu
contamination_sites_ud: contamination_sites_ud
input_bam: sorted_bam
ref_fasta: indexed_reference_fasta
output_basename: output_basename
out: [output]
checkcontamination:
run: ../tools/expression_checkcontamination.cwl
in:
verifybamid_selfsm: verifybamid/output
out: [contamination]
gatk_haplotypecaller:
run: ../tools/gatk_haplotypecaller.cwl
in:
contamination: checkcontamination/contamination
input_bam: picard_gatherbamfiles/output
interval_list: picard_intervallisttools/output
reference: indexed_reference_fasta
scatter: [interval_list]
out: [output]
picard_mergevcfs:
run: ../tools/picard_mergevcfs.cwl
in:
input_vcf: gatk_haplotypecaller/output
output_vcf_basename: output_basename
out: [output]
snpeff_g_vcf:
run: ../tools/snpeff-workflow.cwl
in:
genome: genome
infile: picard_mergevcfs/output
out: [outfile, statsfile, genesfile]
picard_collectgvcfcallingmetrics:
run: ../tools/picard_collectgvcfcallingmetrics.cwl
in:
dbsnp_vcf: dbsnp_vcf
final_gvcf_base_name: output_basename
input_vcf: picard_mergevcfs/output
reference_dict: reference_dict
wgs_evaluation_interval_list: wgs_evaluation_interval_list
out: [output]
$namespaces:
sbg: https://sevenbridges.com
hints:
- class: 'sbg:AWSInstanceType'
value: c4.8xlarge;ebs-gp2;850
- class: 'sbg:maxNumberOfParallelInstances'
value: 4