detect_cross_contamination_precalled_vcfs

WORKFLOW detect_cross_contamination_precalled_vcfs

File Path	`pipes/WDL/workflows/detect_cross_contamination_precalled_vcfs.wdl`
WDL Version	1.0
Type	workflow

Imports

Namespace	Path
`intrahost`	`../tasks/tasks_intrahost.wdl`

Workflow: detect_cross_contamination_precalled_vcfs

Detect cross-contamination between samples using consensus-level and sub-consensus variation, from consensus genomes and pre-called LoFreq vcf files.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`lofreq_vcfs`	`Array[File]+`	per-sample variant call files (VCF) called by LoFreq against reference_fasta	-
`genome_fastas`	`Array[File]+`	consensus sequences, one per file in aligned_bams, in corresponding order	-
`reference_fasta`	`File`	Reference genome to which reads have been aligned, needed here for variant calling	-
`read_depths`	`Array[File]?`	-	-
`masked_positions`	`String?`	-	-
`masked_positions_file`	`File?`	-	-
`plate_maps`	`Array[File]?`	-	-
`plate_columns`	`Int?`	-	-
`plate_rows`	`Int?`	-	-
17 optional inputs with default values
`min_readcount`	`Int`	-	0
`min_maf`	`Float`	-	0
`min_genome_coverage`	`Float`	-	0.95
`min_read_depth`	`Int`	-	100
`max_mismatches`	`Int`	-	0
`min_matches`	`Int`	-	3
`min_matches_proportion`	`Float`	-	1
`plate_size`	`Int?`	-	96
`compare_direct_neighbors`	`Boolean?`	-	true
`compare_diagonal_neighbors`	`Boolean?`	-	false
`compare_full_row`	`Boolean?`	-	false
`compare_full_column`	`Boolean?`	-	false
`compare_full_plate`	`Boolean?`	-	false
`print_all_isnvs`	`Boolean?`	-	true
`print_all`	`Boolean?`	-	false
`out_basename`	`String`	-	"potential_cross_contamination"
`docker`	`String`	-	"quay.io/broadinstitute/polyphonia:latest"

Outputs

Name	Type	Expression
`contamination_report`	`File`	`detect_cross_contam.report`
`contamination_figures`	`Array[File]`	`detect_cross_contam.figures`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `detect_cross_contam` ↗ → polyphonia_detect_cross_contamination

Input Mappings (3)

Input	Value
`lofreq_vcfs`	`lofreq_vcfs`
`genome_fastas`	`genome_fastas`
`reference_fasta`	`reference_fasta`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

detect_cross_contam

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flowchart TD
    Start([detect_cross_contamination_precalled_vcfs])
    N1["detect_cross_contam
polyphonia_detect_cross_contamination"]
    Start --> N1
    N1 --> End([End])
    classDef taskNode fill:#a371f7,stroke:#8b5cf6,stroke-width:2px,color:#fff
    classDef workflowNode fill:#58a6ff,stroke:#1f6feb,stroke-width:2px,color:#fff

version 1.0

import "../tasks/tasks_intrahost.wdl" as intrahost

workflow detect_cross_contamination_precalled_vcfs {
    meta {
        description: "Detect cross-contamination between samples using consensus-level and sub-consensus variation, from consensus genomes and pre-called LoFreq vcf files."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    parameter_meta {
        lofreq_vcfs: {
            description: "per-sample variant call files (VCF) called by LoFreq against reference_fasta",
            patterns: ["*.vcf","*.vcf.gz"]
        }
        genome_fastas: {
            description: "consensus sequences, one per file in aligned_bams, in corresponding order",
            patterns: ["*.fasta"]
        }
        reference_fasta: {
            description: "Reference genome to which reads have been aligned, needed here for variant calling",
            patterns: ["*.fasta"]
        }

    }

    input {
        Array[File]+ lofreq_vcfs
        Array[File]+ genome_fastas
        File         reference_fasta
    }

    call intrahost.polyphonia_detect_cross_contamination as detect_cross_contam {
        input:
            lofreq_vcfs     = lofreq_vcfs,
            genome_fastas   = genome_fastas,
            reference_fasta = reference_fasta
    }

    output {
        File        contamination_report  = detect_cross_contam.report
        Array[File] contamination_figures = detect_cross_contam.figures
        # commented out until polyphonia can report its own version
        #String      polyphonia_version    = detect_cross_contam.polyphonia_version
    }
}