singleton.wdl inputs and outputs

• singleton.wdl inputs and outputs
  • DAG (simplified)
  • Inputs
  • Outputs
    • Alignments, Coverage, and QC
    • Small Variants (<50 bp)
    • Structural Variants (≥50 bp)
    • Copy Number Variants (≥100 kb)
    • Tandem Repeat Genotyping
    • Variant Phasing
    • Variant Calling in Dark Regions
    • 5mCpG Methylation Calling
    • PGx Typing
    • Tertiary Analysis

DAG (simplified)

---
title: singleton.wdl
---
flowchart TD
  subgraph "`**Upstream of Phasing**`"
    subgraph "per-movie"
      ubam[/"HiFi uBAM"/] --> pbmm2_align["pbmm2 align"]
      pbmm2_align --> pbsv_discover["PBSV discover"]
    end
    pbmm2_align --> merge_read_stats["merge read statistics"]
    pbmm2_align --> samtools_merge["samtools merge"]
    samtools_merge --> mosdepth["mosdepth"]
    samtools_merge --> paraphase["Paraphase"]
    samtools_merge --> hificnv["HiFiCNV"]
    samtools_merge --> trgt["TRGT"]
    samtools_merge --> trgt_dropouts["TR coverage dropouts"]
    samtools_merge --> deepvariant["DeepVariant"]
    samtools_merge --> hiphase["HiPhase"]
    pbsv_discover --> pbsv_call["PBSV call"]
  end
  subgraph "`**Phasing and Downstream**`"
    deepvariant --> hiphase
    trgt --> hiphase
    pbsv_call --> hiphase
    hiphase --> bcftools_roh["bcftools roh"]
    hiphase --> bcftools_stats["bcftools stats\n(small variants)"]
    hiphase --> sv_stats["SV stats"]
    hiphase --> cpg_pileup["5mCpG pileup"]
    hiphase --> starphase["StarPhase"]
    hiphase --> pharmcat["PharmCat"]
    starphase --> pharmcat
  end
  subgraph "`**Tertiary Analysis**`"
    hiphase --> slivar_small_variants["slivar small variants"]
    hiphase --> svpack["svpack filter and annotate"]
    svpack --> slivar_svpack["slivar svpack tsv"]
  end

Inputs

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | String | sample_id | Unique identifier for the sample | Alphanumeric characters, periods, dashes, and underscores are allowed. | | String? | sex | Sample sex
["MALE", "FEMALE"] | Used by HiFiCNV and TRGT for genotyping. Allosome karyotype will default to XX unless sex is specified as "MALE". | | Array[File] | hifi_reads | Array of paths to HiFi reads in unaligned BAM format. | | | File | ref_map_file | TSV containing reference genome file paths; must match backend | | | String? | phenotypes | Comma-delimited list of HPO terms. | Human Phenotype Ontology (HPO) phenotypes associated with the cohort.

If omitted, tertiary analysis will be skipped. | | File? | tertiary_map_file | TSV containing tertiary analysis file paths and thresholds; must match backend | AF/AC/nhomalt thresholds can be modified, but this will affect performance.

If omitted, tertiary analysis will be skipped. | | Boolean | gpu | Use GPU when possible

Default: false | GPU support | | String | backend | Backend where the workflow will be executed

["GCP", "Azure", "AWS-AGC", "AWS-HealthOmics", "HPC"] | | | String? | zones | Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'. | Determining available zones in GCP | | String? | gpuType | GPU type to use; required if gpu is set to true for cloud backends; must match backend | Available GPU types | | String? | container_registry | Container registry where workflow images are hosted.

Default: "quay.io/pacbio" | If omitted, PacBio's public Quay.io registry will be used.

Custom container_registry must be set if backend is set to 'AWS-HealthOmics'. | | Boolean | preemptible | Where possible, run tasks preemptibly

[true, false]

Default: true | If set to true, run tasks preemptibly where possible. If set to false, on-demand VMs will be used for every task. Ignored if backend is set to HPC. |

Outputs

Alignments, Coverage, and QC

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | String | workflow_name | Workflow name | | | String | workflow_version | Workflow version | | | File | stats_file | Table of summary statistics | | | File | bam_stats | BAM stats | Per-read length and read-quality | | File | read_length_plot | Read length plot | | | File? | read_quality_plot | Read quality plot | | | File | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads | | File | merged_haplotagged_bam_index | | | | File | mosdepth_summary | Summary of aligned read depth. | | | File | mosdepth_region_bed | Median aligned read depth by 500bp windows. | | | File | mosdepth_region_bed_index | | | | File | mosdepth_depth_distribution_plot | | | | File | mapq_distribution_plot | Distribution of mapping quality per alignment | | | File | mg_distribution_plot | Distribution of gap-compressed identity score per alignment | | | String | stat_num_reads | Number of reads | | | String | stat_read_length_mean | Mean read length | | | String | stat_read_length_median | Median read length | | | String | stat_read_quality_mean | Mean read quality | | | String | stat_read_quality_median | Median read quality | | | String | stat_mapped_read_count | Count of reads mapped to reference | | | String | stat_mapped_percent | Percent of reads mapped to reference | | | String | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. | | String | stat_mean_depth | Mean depth | |

Small Variants (<50 bp)

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | phased_small_variant_vcf | Phased small variant VCF | | | File | phased_small_variant_vcf_index | | | | File | small_variant_gvcf | Small variant GVCF | Can be used for joint-calling. | | File | small_variant_gvcf_index | | | | File | small_variant_stats | Small variant stats | Generated by bcftools stats. | | String | stat_small_variant_SNV_count | SNV count | (PASS variants) | | String | stat_small_variant_INDEL_count | INDEL count | (PASS variants) | | String | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) | | String | stat_small_variant_HETHOM_ratio | Het/Hom ratio | (PASS variants) | | File | snv_distribution_plot | Distribution of SNVs by REF, ALT | | | File | indel_distribution_plot | Distribution of indels by size | |

Structural Variants (≥50 bp)

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | phased_sv_vcf | Phased structural variant VCF | | | File | phased_sv_vcf_index | Index for phased structural variant VCF | | | String | stat_sv_DUP_count | Structural variant DUP count | (PASS variants) | | String | stat_sv_DEL_count | Structural variant DEL count | (PASS variants) | | String | stat_sv_INS_count | Structural variant INS count | (PASS variants) | | String | stat_sv_INV_count | Structural variant INV count | (PASS variants) | | String | stat_sv_BND_count | Structural variant BND count | (PASS variants) | | File | bcftools_roh_out | ROH calling | bcftools roh | | File | bcftools_roh_bed | Generated from above, without filtering | |

Copy Number Variants (≥100 kb)

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | cnv_vcf | CNV VCF | | | File | cnv_vcf_index | Index for CNV VCF | | | File | cnv_copynum_bedgraph | CNV copy number BEDGraph | | | File | cnv_depth_bw | CNV depth BigWig | | | File | cnv_maf_bw | CNV MAF BigWig | | | String | stat_cnv_DUP_count | Count of DUP events | (for PASS variants) | | String | stat_cnv_DEL_count | Count of DEL events | (PASS variants) | | String | stat_cnv_DUP_sum | Sum of DUP bp | (PASS variants) | | String | stat_cnv_DEL_sum | Sum of DEL bp | (PASS variants) |

Tandem Repeat Genotyping

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | phased_trgt_vcf | Phased TRGT VCF | | | File | phased_trgt_vcf_index | | | | File | trgt_spanning_reads | TRGT spanning reads | | | File | trgt_spanning_reads_index | | | | File | trgt_coverage_dropouts | TRGT coverage dropouts | | | String | stat_trgt_genotyped_count | Count of genotyped sites | | | String | stat_trgt_uncalled_count | Count of ungenotyped sites | |

Variant Phasing

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | phase_stats | Phasing stats | | | File | phase_blocks | Phase blocks | | | File | phase_haplotags | Per-read haplotag assignment | | | String | stat_phased_basepairs | Count of bp within phase blocks | | | String | stat_phase_block_ng50 | Phase block NG50 | |

Variant Calling in Dark Regions

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | paraphase_output_json | Paraphase output JSON | | | File | paraphase_realigned_bam | Paraphase realigned BAM | | | File | paraphase_realigned_bam_index | | | | File? | paraphase_vcfs | Paraphase VCFs | Compressed as .tar.gz |

5mCpG Methylation Calling

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File? | cpg_hap1_bed | CpG hap1 BED | | | File? | cpg_hap1_bed_index | | | | File? | cpg_hap2_bed | CpG hap2 BED | | | File? | cpg_hap2_bed_index | | | | File? | cpg_combined_bed | CpG combined BED | | | File? | cpg_combined_bed_index | | | | File? | cpg_hap1_bw | CpG hap1 BigWig | | | File? | cpg_hap2_bw | CpG hap2 BigWig | | | File? | cpg_combined_bw | CpG combined BigWig | | | String | stat_cpg_hap1_count | Hap1 CpG count | | | String | stat_cpg_hap2_count | Hap2 CpG count | | | String | stat_cpg_combined_count | Combined CpG count | |

PGx Typing

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci | | File? | pharmcat_match_json | PharmCAT match JSON | | | File? | pharmcat_phenotype_json | PharmCAT phenotype JSON | | | File? | pharmcat_report_html | PharmCAT report HTML | | | File? | pharmcat_report_json | PharmCAT report JSON | |

Tertiary Analysis

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File? | pedigree | Pedigree file in PLINK PED format | | | File? | tertiary_small_variant_filtered_vcf | Filtered, annotated small variant VCF | | | File? | tertiary_small_variant_filtered_vcf_index | | | | File? | tertiary_small_variant_filtered_tsv | Filtered, annotated small variant calls | | | File? | tertiary_small_variant_compound_het_vcf | Filtered, annotated compound heterozygous small variant VCF | | | File? | tertiary_small_variant_compound_het_vcf_index | | | | File? | tertiary_small_variant_compound_het_tsv | Filtered, annotated compound heterozygous small variant calls | | | File? | tertiary_sv_filtered_vcf | Filtered, annotated structural variant VCF | | | File? | tertiary_sv_filtered_vcf_index | | | | File? | tertiary_sv_filtered_tsv | Filtered, annotated structural variant TSV | |