HPVDeepSeek v0-prerelease

.dockstore.yml

@@ -153,3 +153,18 @@ workflows:
   - name: CNVControlEventsQC
     subclass: WDL
     primaryDescriptorPath: /gCNV/CNVControlEventsQC.wdl
+  - name: HPVDeepSeek
+    subclass: WDL
+    primaryDescriptorPath: /HPVDeepSeek/HPVDeepSeek.wdl
+  - name: HPVDeepSeekGenotyping
+    subclass: WDL
+    primaryDescriptorPath: /HPVDeepSeek/HPVDeepSeekGenotyping.wdl
+  - name: HPVDeepSeekSomaticVariantCalling
+    subclass: WDL
+    primaryDescriptorPath: /HPVDeepSeek/HPVDeepSeekSomaticVariantCalling.wdl
+  - name: HPVDeepSeekTertiaryAnalysis
+    subclass: WDL
+    primaryDescriptorPath: /HPVDeepSeek/HPVDeepSeekTertiaryAnalysis.wdl
+  - name: HPVDeepSeekNormalization
+    subclass: WDL
+    primaryDescriptorPath: /HPVDeepSeek/HPVDeepSeekNormalization.wdl

HPVDeepSeek/HPVDeepSeek.wdl

@@ -0,0 +1,183 @@
+version 1.0
+
+import "HPVDeepSeekGenotyping.wdl" as HPVDeepSeekGenotyping
+import "HPVDeepSeekSomaticVariantCalling.wdl" as HPVDeepSeekSomaticVariantCalling
+import "HPVDeepSeekTertiaryAnalysis.wdl" as HPVDeepSeekTertiaryAnalysis
+
+workflow HPVDeepSeek {
+    input {
+        # HPVDeepSeekGenotyping inputs
+        String output_basename
+        File r1_fastq
+        File r2_fastq
+        File human_snp_targets_bed
+        File reference
+        File reference_fai
+        File reference_dict
+        File bwa_idx_amb
+        File bwa_idx_ann
+        File bwa_idx_bwt
+        File bwa_idx_pac
+        File bwa_idx_sa
+        File capture_targets_bed
+        File bait_interval_list
+        File target_interval_list
+        String bait_set_name
+        String read_group_id
+        String read_group_sample_name
+        String read_group_library_name = "LB_TEST"
+        String read_group_platform = "ILLUMINA"
+        String read_group_platform_unit = "PU_TEST"
+        String read_group_description = "KAPA_TE"
+
+        # HPVDeepSeekSomaticVariantCalling inputs
+        File target_intervals
+        File gnomad
+        File gnomad_idx
+        File pon
+        File pon_idx
+        File variants_for_contamination
+        File variants_for_contamination_idx
+        File realignment_index_bundle
+        String mapping_filter_python_script = "/usr/filter_alt_ref_positions.py"
+        File blastdb_nhr
+        File blastdb_nin
+        File blastdb_nsq
+        String blastn_path = "/usr/blastn_2.2.30+"
+        File funcotator_data_source
+        Boolean run_alignment_artifact_filter = false
+
+        # HPVDeepSeekTertiaryAnalysis inputs
+        File high_risk_snps_hpv
+        File hpv16_sublineages
+    }
+
+    call HPVDeepSeekGenotyping.HPVDeepSeekGenotyping {
+        input:
+            output_basename = output_basename,
+            r1_fastq = r1_fastq,
+            r2_fastq = r2_fastq,
+            human_snp_targets_bed = human_snp_targets_bed,
+            reference = reference,
+            reference_fai = reference_fai,
+            reference_dict = reference_dict,
+            bwa_idx_amb = bwa_idx_amb,
+            bwa_idx_ann = bwa_idx_ann,
+            bwa_idx_bwt = bwa_idx_bwt,
+            bwa_idx_pac = bwa_idx_pac,
+            bwa_idx_sa = bwa_idx_sa,
+            capture_targets_bed = capture_targets_bed,
+            bait_interval_list = bait_interval_list,
+            target_interval_list = target_interval_list,
+            bait_set_name = bait_set_name,
+            read_group_id = read_group_id,
+            read_group_sample_name = read_group_sample_name,
+            read_group_library_name = read_group_library_name,
+            read_group_platform = read_group_platform,
+            read_group_platform_unit = read_group_platform_unit,
+            read_group_description = read_group_description
+    }
+
+    call HPVDeepSeekSomaticVariantCalling.HPVDeepSeekSomaticVariantCalling {
+        input:
+            output_basename = output_basename,
+            tumor_bam = HPVDeepSeekGenotyping.final_bam,
+            tumor_bai = HPVDeepSeekGenotyping.final_bam_index,
+            target_intervals = target_intervals,
+            reference = reference,
+            reference_fai = reference_fai,
+            reference_dict = reference_dict,
+            gnomad = gnomad,
+            gnomad_idx = gnomad_idx,
+            pon = pon,
+            pon_idx = pon_idx,
+            variants_for_contamination = variants_for_contamination,
+            variants_for_contamination_idx = variants_for_contamination_idx,
+            realignment_index_bundle = realignment_index_bundle,
+            mapping_filter_python_script = mapping_filter_python_script,
+            blastdb_nhr = blastdb_nhr,
+            blastdb_nin = blastdb_nin,
+            blastdb_nsq = blastdb_nsq,
+            blastn_path = blastn_path,
+            funcotator_data_source = funcotator_data_source,
+            run_alignment_artifact_filter = run_alignment_artifact_filter
+    }
+
+    call HPVDeepSeekTertiaryAnalysis.HPVDeepSeekTertiaryAnalysis {
+        input:
+            output_basename = output_basename,
+            tumor_bam = HPVDeepSeekGenotyping.final_bam,
+            tumor_bai = HPVDeepSeekGenotyping.final_bam_index,
+            high_risk_snps_hpv = high_risk_snps_hpv,
+            reference = reference,
+            reference_fai = reference_fai,
+            reference_dict = reference_dict,
+            hpv16_sublineages = hpv16_sublineages
+    }
+
+    output {
+        # HPVDeepSeekGenotyping outputs
+        File raw_bam = HPVDeepSeekGenotyping.raw_bam
+        File raw_bam_index = HPVDeepSeekGenotyping.raw_bam_index
+        File final_bam = HPVDeepSeekGenotyping.final_bam
+        File final_bam_index = HPVDeepSeekGenotyping.final_bam_index
+        File umi_grouped_bam = HPVDeepSeekGenotyping.umi_grouped_bam
+        File umi_group_data = HPVDeepSeekGenotyping.umi_group_data
+        File umi_duplication_metrics = HPVDeepSeekGenotyping.umi_duplication_metrics
+        File vcf = HPVDeepSeekGenotyping.vcf
+        File coverage = HPVDeepSeekGenotyping.coverage
+        String top_hpv_contig = HPVDeepSeekGenotyping.top_hpv_contig
+        Int top_hpv_num_reads = HPVDeepSeekGenotyping.top_hpv_num_reads
+        Float top_hpv_coverage = HPVDeepSeekGenotyping.top_hpv_coverage
+        Boolean is_hpv_positive = HPVDeepSeekGenotyping.is_hpv_positive
+        String secondary_hpv_types = HPVDeepSeekGenotyping.secondary_hpv_types
+        File fastp_report_html = HPVDeepSeekGenotyping.fastp_report_html
+        File fastp_report_json = HPVDeepSeekGenotyping.fastp_report_json
+        File pre_trimmed_r1_fastqc_html = HPVDeepSeekGenotyping.pre_trimmed_r1_fastqc_html
+        File pre_trimmed_r2_fastqc_html = HPVDeepSeekGenotyping.pre_trimmed_r2_fastqc_html
+        File post_trimmed_r1_fastqc_html = HPVDeepSeekGenotyping.post_trimmed_r1_fastqc_html
+        File post_trimmed_r2_fastqc_html = HPVDeepSeekGenotyping.post_trimmed_r2_fastqc_html
+        File pre_consensus_alignment_summary_metrics = HPVDeepSeekGenotyping.pre_consensus_alignment_summary_metrics
+        File pre_consensus_flagstat = HPVDeepSeekGenotyping.pre_consensus_flagstat
+        File pre_consensus_insert_size_metrics = HPVDeepSeekGenotyping.pre_consensus_insert_size_metrics
+        File pre_consensus_insert_size_plot = HPVDeepSeekGenotyping.pre_consensus_insert_size_plot
+        File pre_consensus_ontarget_reads = HPVDeepSeekGenotyping.pre_consensus_ontarget_reads
+        File pre_consensus_hs_metrics = HPVDeepSeekGenotyping.pre_consensus_hs_metrics
+        File pre_consensus_per_base_coverage = HPVDeepSeekGenotyping.pre_consensus_per_base_coverage
+        File post_consensus_alignment_summary_metrics = HPVDeepSeekGenotyping.post_consensus_alignment_summary_metrics
+        File post_consensus_flagstat = HPVDeepSeekGenotyping.post_consensus_flagstat
+        File post_consensus_insert_size_metrics = HPVDeepSeekGenotyping.post_consensus_insert_size_metrics
+        File post_consensus_insert_size_plot = HPVDeepSeekGenotyping.post_consensus_insert_size_plot
+        File post_consensus_ontarget_reads = HPVDeepSeekGenotyping.post_consensus_ontarget_reads
+        File post_consensus_hs_metrics = HPVDeepSeekGenotyping.post_consensus_hs_metrics
+        File post_consensus_per_base_coverage = HPVDeepSeekGenotyping.post_consensus_per_base_coverage
+        File? family_sizes = HPVDeepSeekGenotyping.family_sizes
+        File? duplex_family_sizes = HPVDeepSeekGenotyping.duplex_family_sizes
+        File? duplex_yield_metrics = HPVDeepSeekGenotyping.duplex_yield_metrics
+        File? umi_counts = HPVDeepSeekGenotyping.umi_counts
+        File? duplex_qc = HPVDeepSeekGenotyping.duplex_qc
+
+        # HPVDeepSeekSomaticVariantCalling outputs
+        File unfiltered_vcf = HPVDeepSeekSomaticVariantCalling.unfiltered_vcf
+        File unfiltered_vcf_idx = HPVDeepSeekSomaticVariantCalling.unfiltered_vcf_idx
+        File mutect2_stats = HPVDeepSeekSomaticVariantCalling.mutect2_stats
+        File filter_mutect_calls_stats = HPVDeepSeekSomaticVariantCalling.filter_mutect_calls_stats
+        File filtered_vcf = HPVDeepSeekSomaticVariantCalling.filtered_vcf
+        File filtered_vcf_idx = HPVDeepSeekSomaticVariantCalling.filtered_vcf_idx
+        File funcotated_maf = HPVDeepSeekSomaticVariantCalling.funcotated_maf
+
+        # HPVDeepSeekTertiaryAnalysis outputs
+        File analysis_log = HPVDeepSeekTertiaryAnalysis.analysis_log
+        File breakpoints = HPVDeepSeekTertiaryAnalysis.breakpoints
+        File detailed_integration_summary = HPVDeepSeekTertiaryAnalysis.detailed_integration_summary
+        File integration_breakpoints = HPVDeepSeekTertiaryAnalysis.integration_breakpoints
+        File integration_summary = HPVDeepSeekTertiaryAnalysis.integration_summary
+        File multiple_sequence_alignment = HPVDeepSeekTertiaryAnalysis.multiple_sequence_alignment
+        File phylip_formatted_msa = HPVDeepSeekTertiaryAnalysis.phylip_formatted_msa
+        File phylogenetic_tree_stats = HPVDeepSeekTertiaryAnalysis.phylogenetic_tree_stats
+        File phylogenetic_tree = HPVDeepSeekTertiaryAnalysis.phylogenetic_tree
+        File phylogenetic_tree_visualization = HPVDeepSeekTertiaryAnalysis.phylogenetic_tree_visualization
+        File sublineage_call = HPVDeepSeekTertiaryAnalysis.sublineage_call
+        File high_risk_snps_found = HPVDeepSeekTertiaryAnalysis.high_risk_snps_found
+    }
+}