forked from kids-first/kf-alignment-workflow
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kfdrc_cram_reheader_wf.cwl
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/
kfdrc_cram_reheader_wf.cwl
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cwlVersion: v1.0
class: Workflow
id: kfdrc_cram_reheader
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
input_cram: File
biospecimen_name: string
output_basename: string
indexed_reference_fasta: File
dbsnp_vcf: 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
outputs:
cram: {type: File, outputSource: samtools_covert_to_cram_dev/output}
gvcf: {type: File, outputSource: picard_mergevcfs/output}
verifybamid_output: {type: File, outputSource: verifybamid/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}
steps:
samtools_cram_reheader:
run: ../tools/samtools_cram_reheader.cwl
in:
input_cram: input_cram
base_file_name: biospecimen_name
output_basename: output_basename
reference: indexed_reference_fasta
out: [output]
samtools_covert_to_cram_dev:
run: ../tools/samtools_covert_to_cram_dev.cwl
in:
input_bam: samtools_cram_reheader/output
reference: indexed_reference_fasta
output_basename: output_basename
out: [output]
picard_collectaggregationmetrics:
run: ../tools/picard_collectaggregationmetrics.cwl
in:
input_bam: samtools_cram_reheader/output
reference: indexed_reference_fasta
out: [output]
picard_collectwgsmetrics:
run: ../tools/picard_collectwgsmetrics.cwl
in:
input_bam: samtools_cram_reheader/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: samtools_cram_reheader/output
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: samtools_cram_reheader/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]
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