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kfdrc_alignment_pipeline.cwl
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kfdrc_alignment_pipeline.cwl
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cwlVersion: v1.0
class: Workflow
id: kfdrc_alignment_pipeline
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
input_bam: File
output_basename: string
indexed_reference_fasta: File
contamination_sites_ud: File
contamination_sites_mu: File
contamination_sites_bed: File
knownsites: File[]
wgs_coverage_interval_list: File
wgs_calling_interval_list: File
reference_dict: File
wgs_evaluation_interval_list: File
dbsnp_vcf: File
outputs:
bqsr_report: {type: File, outputSource: gatk_gatherbqsrreports/output}
final_bam: {type: File, outputSource: picard_gatherbamfiles/output}
gvcf: {type: File, outputSource: picard_mergevcfs/output}
cram: {type: File, outputSource: samtools_coverttocram/output}
verifybamid_output: {type: File, outputSource: verifybamid/output}
collect_quality_yield_metrics: {type: 'File[]', outputSource: picard_collectqualityyieldmetrics/output}
collect_collect_aggregation_metrics: {type: 'File[]', outputSource: picard_collectaggregationmetrics/output}
collect_wgs_metrics: {type: File, outputSource: picard_collectwgsmetrics/output}
calculate_readgroup_checksum: {type: File, outputSource: picard_calculatereadgroupchecksum/output}
collect_readgroupbam_quality_metrics: {type: 'File[]', outputSource: picard_collectreadgroupbamqualitymetrics/output}
picard_collect_gvcf_calling_metrics: {type: 'File[]', outputSource: picard_collectgvcfcallingmetrics/output}
steps:
picard_revertsam:
run: ../tools/picard_revertsam.cwl
in:
input_bam: input_bam
reference: indexed_reference_fasta
out: [output]
picard_collectqualityyieldmetrics:
run: ../tools/picard_collectqualityyieldmetrics.cwl
in:
input_bam: picard_revertsam/output
output_basename: output_basename
scatter: [input_bam]
out: [output]
bwa_mem:
run: ../tools/bwa_mem.cwl
in:
indexed_reference_fasta: indexed_reference_fasta
input_bam: picard_revertsam/output
scatter: [input_bam]
out: [output]
picard_markduplicates:
run: ../tools/picard_markduplicates.cwl
in:
base_file_name: output_basename
input_bams: bwa_mem/output
out: [output_markduplicates_bam]
picard_sortsam:
run: ../tools/picard_sortsam.cwl
in:
base_file_name: output_basename
input_bam: picard_markduplicates/output_markduplicates_bam
out: [output_sorted_bam]
verifybamid:
run: ../tools/verifybamid.cwl
in:
input_bam: picard_sortsam/output_sorted_bam
ref_fasta: indexed_reference_fasta
contamination_sites_ud: contamination_sites_ud
contamination_sites_mu: contamination_sites_mu
contamination_sites_bed: contamination_sites_bed
output_basename: output_basename
out: [output]
createsequencegrouping:
run: ../tools/python_createsequencegroups.cwl
in:
ref_dict: reference_dict
out: [out_intervals]
gatk_baserecalibrator:
run: ../tools/gatk_baserecalibrator.cwl
in:
input_bam: picard_sortsam/output_sorted_bam
knownsites: knownsites
reference: indexed_reference_fasta
sequence_interval: createsequencegrouping/out_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:
reference: indexed_reference_fasta
input_bam: picard_sortsam/output_sorted_bam
bqsr_report: gatk_gatherbqsrreports/output
sequence_interval: createsequencegrouping/out_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_collectreadgroupbamqualitymetrics:
run: ../tools/picard_collectreadgroupbamqualitymetrics.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
reference: indexed_reference_fasta
intervals: wgs_coverage_interval_list
out: [output]
picard_calculatereadgroupchecksum:
run: ../tools/picard_calculatereadgroupchecksum.cwl
in:
input_bam: picard_gatherbamfiles/output
out: [output]
samtools_coverttocram:
run: ../tools/samtools_covert_to_cram.cwl
in:
input_bam: picard_gatherbamfiles/output
reference: indexed_reference_fasta
out: [output]
picard_intervallisttools:
run: ../tools/picard_intervallisttools.cwl
in:
interval_list: wgs_calling_interval_list
out: [output]
checkcontamination:
run: ../tools/expression_checkcontamination.cwl
in:
verifybamid_selfsm: verifybamid/output
out: [contamination]
gatk_haplotypecaller:
run: ../tools/gatk_haplotypecaller.cwl
in:
reference: indexed_reference_fasta
input_bam: picard_gatherbamfiles/output
interval_list: picard_intervallisttools/output
contamination: checkcontamination/contamination
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:
input_vcf: picard_mergevcfs/output
reference_dict: reference_dict
final_gvcf_base_name: output_basename
dbsnp_vcf: dbsnp_vcf
wgs_evaluation_interval_list: wgs_evaluation_interval_list
out: [output]
gatk_validategvcf:
run: ../tools/gatk_validategvcf.cwl
in:
input_vcf: picard_mergevcfs/output
reference: indexed_reference_fasta
wgs_calling_interval_list: wgs_calling_interval_list
dbsnp_vcf: dbsnp_vcf
out: []
$namespaces:
sbg: https://sevenbridges.com
hints:
- class: 'sbg:AWSInstanceType'
value: c5.9xlarge;ebs-gp2;768
- class: 'sbg:maxNumberOfParallelInstances'
value: 4