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)
    • 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 "create fail_reads bait FASTA"
    trgt_catalog["TRGT catalog BED"]
    bait_fasta["create bait FASTA"]
  end
  subgraph "`**Upstream of Phasing**`"
    subgraph "per hifi_reads uBAM"
      ubam[/"HiFi uBAM"/]
      pbmm2_align["pbmm2 align"]
    end
    subgraph "per fail_reads uBAM"
      fail_ubam[/"fail reads uBAM (if provided)"/]
      bait_fail_reads["baited fail reads (if fail_reads provided)"]
      pbmm2_align_fail_reads["pbmm2 align baited fail_reads (if fail_reads provided)"]
      filter_fail_reads["filter fail_reads alignments (if fail_reads provided)"]
    end
    samtools_merge["samtools merge"]
    mosdepth["mosdepth"]
    paraphase["Paraphase"]
    mitorsaw["MitorSaw"]
    deepvariant["DeepVariant"]
    sawfish_discover["Sawfish discover"]
    sawfish_call["Sawfish call"]
  end
  subgraph "`**Phasing and Downstream**`"
    hiphase["HiPhase"]
    samtools_merge_fail_reads["samtools merge phased hifi_reads and aligned fail_reads"]
    trgt["TRGT"]
    bam_stats["BAM stats"]
    bcftools_roh["bcftools roh"]
    bcftools_stats["bcftools stats\n(small variants)"]
    sv_stats["SV stats"]
    cpg_pileup["5mCpG pileup"]
    methbat["MethBat"]
    starphase["StarPhase"]
    pharmcat["PharmCat"]
  end
  subgraph "`**Tertiary Analysis**`"
    slivar_small_variants["slivar small variants"]
    svpack["svpack filter and annotate"]
    slivar_svpack["slivar svpack tsv"]
  end

  trgt_catalog --> bait_fasta --> bait_fail_reads
  fail_ubam --> bait_fail_reads --> pbmm2_align_fail_reads --> filter_fail_reads --> samtools_merge_fail_reads
  ubam --> pbmm2_align --> samtools_merge
  samtools_merge --> mosdepth
  samtools_merge --> paraphase
  samtools_merge --> mitorsaw
  samtools_merge_fail_reads --> trgt
  samtools_merge --> deepvariant
  samtools_merge --> sawfish_discover
  samtools_merge --> hiphase
  deepvariant --> sawfish_discover
  deepvariant --> hiphase
  sawfish_discover --> sawfish_call --> hiphase

  hiphase --> trgt
  hiphase --> bam_stats
  hiphase --> bcftools_roh
  hiphase --> bcftools_stats
  hiphase --> sv_stats
  hiphase --> cpg_pileup
  hiphase --> starphase
  hiphase --> pharmcat
  hiphase --> trgt_dropouts
  starphase --> pharmcat
  cpg_pileup --> methbat

  hiphase --> slivar_small_variants
  hiphase --> svpack
  svpack --> slivar_svpack

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. | | | Array[File]? | fail_reads | Array of paths to fail_reads in unaligned BAM format (optional) | If provided, these reads will be aligned to the bait-captured regions. | | 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. | | Int | max_reads_per_alignment_chunk | Maximum reads per alignment chunk

Default: 500000 | | | Int | pharmcat_min_coverage | Minimum coverage for PharmCAT

Default: 10 | | | Boolean | use_gpu | Use GPU when possible

Default: false | GPU support | | Boolean | use_parabricks_deepvariant | Use Parabricks DeepVariant implementation

Default: false | If both use_parabricks_deepvariant and use_gpu are set to true, Parabricks DeepVariant will be used instead of standard DeepVariant.

Parabricks DeepVariant | | String | backend | Backend where the workflow will be executed

["GCP", "Azure", "AWS-HealthOmics", "HPC"] | | | String? | zones | Zones where compute will take place; required if backend is set to 'GCP' | Determining available zones in GCP | | String? | cpuPlatform | Minimum CPU platform to use for tasks on GCP | Optional, only necessary in certain zones lacking n1 nodes. | | String? | gpuType | GPU type to use; required if use_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. | | String? | debug_version | Debug version for testing purposes | |

Outputs

Alignments, Coverage, and QC

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | String | workflow_name | Workflow name | | | String | workflow_version | Workflow version | | | Array[String] | msg | Messages from the workflow | | | File | msg_file | File containing messages from the workflow | | | File | stats_file | Table of summary statistics | | | File | bam_statistics | BAM statistics | Per-read length and read-quality | | File | read_length_plot | Distribution of read lengths | | | File? | read_quality_plot | Distribution of read qualities | | | 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 | Distribution of aligned read depth | | | File | mapq_distribution_plot | Distribution of mapping quality per alignment | | | File | mg_distribution_plot | Distribution of gap-compressed identity per alignment | | | String | stat_read_count | Number of reads | | | String | stat_read_length_mean | Mean read length | | | String | stat_read_length_median | Median read length | | | String | stat_read_length_n50 | Read length N50 | | | String | stat_read_quality_mean | Mean read quality | | | String | stat_read_quality_median | Median read quality | | | String | stat_mapped_read_count | Number of reads mapped to reference | | | String | stat_mapped_read_percent | Percent of reads mapped to reference | | | String | stat_gap_compressed_identity_mean | Mean gap-compressed identity | | | String | stat_gap_compressed_identity_median | Median gap-compressed identity | | | String | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. | | String | stat_depth_mean | 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 statistics | Generated by bcftools stats. | | String | stat_small_variant_SNV_count | Number of SNVs | (PASS variants) | | String | stat_small_variant_INDEL_count | Number of INDELs | (PASS variants) | | String | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) | | String | stat_small_variant_HETHOM_ratio | Het/Hom ratio for SNVs | (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 | Number of DUP structural variants | (PASS variants) | | String | stat_sv_DEL_count | Number of DEL structural variants | (PASS variants) | | String | stat_sv_INS_count | Number of INS structural variants | (PASS variants) | | String | stat_sv_INV_count | Number of INV structural variants | (PASS variants) | | String | stat_sv_BND_count | Number of BND structural variants | (PASS variants) | | String | stat_sv_SWAP_count | Number of structural variant sequence swap events | (PASS variants) | | File | sv_supporting_reads | Supporting reads for structural variants | | | File | sv_copynum_bedgraph | CNV copy number BEDGraph | | | File | sv_depth_bw | CNV depth BigWig | | | File | sv_gc_bias_corrected_depth_bw | CNV GC-bias corrected depth BigWig | | | File | sv_maf_bw | CNV MAF BigWig | | | File | sv_copynum_summary | CNV copy number summary JSON | | | File | bcftools_roh_out | Regions of homozygosity | bcftools roh | | File | bcftools_roh_bed | Regions of homozygosity BED | |

Mitochondrial variants and haplotypes

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | mitorsaw_vcf | Mitochondrial variant VCF | | | File | mitorsaw_vcf_index | Index for mitochondrial variant VCF | | | File | mitorsaw_hap_stats | Mitochondrial haplotype statistics | |

Tandem Repeat Genotyping

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

Variant Phasing

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | phase_stats | Phasing statistics | | | File | phase_blocks | Phase blocks | | | File | phase_haplotags | Per-read phase assignment | | | String | stat_phased_basepairs | Number of basepairs within phase blocks | | | String | stat_phase_block_ng50 | Phase block NG50 | |

Variant Calling in Dark Regions

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File? | paraphase_summary | Paraphase summary | | | File? | paraphase_realigned_bam | BAM file of reads realigned by Paraphase | | | 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 | 5mCpG haplotype 1 BED | | | File? | cpg_hap1_bed_index | | | | File? | cpg_hap2_bed | 5mCpG haplotype 2 BED | | | File? | cpg_hap2_bed_index | | | | File? | cpg_combined_bed | 5mCpG combined BED | | | File? | cpg_combined_bed_index | | | | File? | cpg_hap1_bw | 5mCpG haplotype 1 BigWig | | | File? | cpg_hap2_bw | 5mCpG haplotype 2 BigWig | | | File? | cpg_combined_bw | 5mCpG combined BigWig | | | String | stat_cpg_hap1_count | Number of scored reference 5mCpGs in haplotype 1 | | | String | stat_cpg_hap2_count | Number of scored reference 5mCpGs in haplotype 2 | | | String | stat_cpg_combined_count | Number of scored reference 5mCpGs combined | | | File? | methbat_profile | MethBat 5mCpG profile | | | String | stat_methbat_methylated_count | Number of profiled regions labeled as methylated | | | String | stat_methbat_unmethylated_count | Number of profiled regions labeled as unmethylated | | | String | stat_methbat_asm_count | Number of profiled regions labeled as having allele-specific methylation | |

PGx Typing

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | pbstarphase_summary | StarPhase summary | 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? | 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 TSV | | | 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 TSV | | | 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 | |