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MetaDenovo.wdl
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MetaDenovo.wdl
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import "PhasebytransmissionPipeline.wdl" as PBT_p
import "TrioDenovoPipeline.wdl" as TrioDenovo_p
import "VarScan2Pipeline.wdl" as VarScan2_p
import "DenovoGearPipeline.wdl" as DenovoGear_p
import "ConsensusDNMs.wdl" as consensusDNM_p
workflow MetaDenovo_workflow {
File mother_bam
File mother_bam_bai
File father_bam
File father_bam_bai
File child_bam
File child_bam_bai
Array[Int] chromosome_ids
File reference
File reference_fai
File reference_dict
File ped_file
File gatk_vcf
File python_file
File selectDNMGenotype_program
## Call workflow of Phasebytransmission caller
call PBT_p.PhasebytransmissionPipeline as PBT_p {
input:
gatk_vcf=gatk_vcf,
ped_file=ped_file,
## snpSiftJar=snpSiftJar,
reference=reference,
reference_fai=reference_fai,
reference_dict=reference_dict
}
## Call workflow of TrioDenovo caller
call TrioDenovo_p.TrioDenovoPipeline as TrioDenovo_p {
input:
gatk_vcf=gatk_vcf,
ped_file=ped_file,
## snpSiftJar=snpSiftJar,
selectDNMGenotype_program=selectDNMGenotype_program
}
## Call workflow of DenovoGear caller
call DenovoGear_p.DenovoGearPipeline as DenovoGear_p {
input:
chromosome_ids=chromosome_ids,
reference=reference,
reference_fai=reference_fai,
reference_dict=reference_dict,
father_bam=father_bam,
father_bam_bai=father_bam_bai,
mother_bam=mother_bam,
mother_bam_bai=mother_bam_bai,
child_bam=child_bam,
child_bam_bai=child_bam_bai,
python_file=python_file,
ped_file=ped_file
}
## Call workflow of VarScan2 caller
call VarScan2_p.VarScan2Pipeline as VarScan2_p {
input:
## snpSiftJar=snpSiftJar,
chromosome_ids=chromosome_ids,
reference=reference,
reference_fai=reference_fai,
reference_dict=reference_dict,
father_bam=father_bam,
father_bam_bai=father_bam_bai,
mother_bam=mother_bam,
mother_bam_bai=mother_bam_bai,
child_bam=child_bam,
child_bam_bai=child_bam_bai
}
## Call callConsensusDNMs to generate output files for consensus of de novo SNPs using four, three, two and one callers.
call consensusDNM_p.callConsensusDNMs as consensusDNM_snv {
input:
variant_type = "SNP",
PBT_file = PBT_p.PBT_listof_dnSNPs_file,
TrioDenovo_file = TrioDenovo_p.TrioDenovo_list_of_snps_output,
varScan2_file = VarScan2_p.VarScan2_list_of_snps_output,
DenovoGear_file = DenovoGear_p.DenovoGear_list_of_snps_output
}
## Call callConsensusDNMs to generate output files for consensus of de novo INDELs using four, three, two and one callers.
call consensusDNM_p.callConsensusDNMs as consensusDNM_indel {
input:
variant_type = "INDEL",
PBT_file = PBT_p.PBT_listof_dnINDELs_file,
TrioDenovo_file = TrioDenovo_p.TrioDenovo_list_of_indels_output,
varScan2_file = VarScan2_p.VarScan2_list_of_indels_output,
DenovoGear_file = DenovoGear_p.DenovoGear_list_of_indels_output
}
## Output files generated by the MetaDenovo workflow.
output {
File pbt_output_vcf_file = PBT_p.pbt_output_vcf_file
File mendelViolations_file = PBT_p.mendelViolations_file
File PBT_DNMs_list_Mendel_Violations = PBT_p.PBT_DNMs_list_Mendel_Violations
File PBT_output_file_annotated = PBT_p.PBT_output_file_annotated
File PBT_GenoType_Filtered = PBT_p.PBT_GenoType_Filtered
File bgzip_output_file = PBT_p.bgzip_output_file
File bgzip_index_file = PBT_p.bgzip_index_file
File PBT_Variant_Annotated_Mendel_Violations = PBT_p.PBT_Variant_Annotated_Mendel_Violations
File PBT_listof_dnSNPs_file = PBT_p.PBT_listof_dnSNPs_file
File PBT_listof_dnINDELs_file = PBT_p.PBT_listof_dnINDELs_file
File triodenovo_output_vcf_file = TrioDenovo_p.triodenovo_output_vcf_file
File Triodenovo_output_DQ_datatype = TrioDenovo_p.Triodenovo_output_DQ_datatype
File Triodenovo_chr1_22_vcf = TrioDenovo_p.Triodenovo_chr1_22_vcf
File Triodenovo_output_file_annotated = TrioDenovo_p.Triodenovo_output_file_annotated
File Triodenovo_selected_dnSNV = TrioDenovo_p.Triodenovo_selected_dnSNV
File TrioDenovo_listof_allDNMs_file = TrioDenovo_p.TrioDenovo_listof_allDNMs_file
File TrioDenovo_list_of_snps_output = TrioDenovo_p.TrioDenovo_list_of_snps_output
File TrioDenovo_list_of_indels_output = TrioDenovo_p.TrioDenovo_list_of_indels_output
File CombinedDNGOutput = DenovoGear_p.CombinedDNGOutput
File DenovoGear_NumericGenotype_output = DenovoGear_p.DenovoGear_NumericGenotype_output
File DenovoGear_DNM_Genotype_output = DenovoGear_p.DenovoGear_DNM_Genotype_output
File DenovoGear_snp_file = DenovoGear_p.DenovoGear_snp_file
File DenovoGear_indel_file = DenovoGear_p.DenovoGear_indel_file
File DenovoGear_DNMs_file_output = DenovoGear_p.DenovoGear_DNMs_file_output
File DenovoGear_list_of_snps_output = DenovoGear_p.DenovoGear_list_of_snps_output
File DenovoGear_list_of_indels_output = DenovoGear_p.DenovoGear_list_of_indels_output
File VarScan2_snp_combined = VarScan2_p.VarScan2_snp_combined
File VarScan2_indel_combined = VarScan2_p.VarScan2_indel_combined
File VarScan2_snp_DNMs_file = VarScan2_p.VarScan2_snp_DNMs_file
File VarScan2_indel_DNMs_file = VarScan2_p.VarScan2_indel_DNMs_file
File VarScan2_list_of_snps_output = VarScan2_p.VarScan2_list_of_snps_output
File VarScan2_list_of_indels_output = VarScan2_p.VarScan2_list_of_indels_output
Array[File] consensus_output_snp_files = consensusDNM_snv.output_text_files
Array[File] consensus_output_indel_files = consensusDNM_indel.output_text_files
}
}