align_and_count_report

WORKFLOW align_and_count_report

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

Imports

Namespace	Path
`reports`	`../tasks/tasks_reports.wdl`

Workflow: align_and_count_report

Align reads to reference with minimap2 and count the number of hits. Results are returned in the format of 'samtools idxstats'.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_bam`	`File`	-	-
`ref_db`	`File`	File containing sequences against which reads should me aligned and counted	-
`machine_mem_gb`	`Int?`	-	-
6 optional inputs with default values
`topNHits`	`Int`	-	3
`filter_bam_to_proper_primary_mapped_reads`	`Boolean`	-	true
`do_not_require_proper_mapped_pairs_when_filtering`	`Boolean`	-	false
`keep_singletons_when_filtering`	`Boolean`	-	false
`keep_duplicates_when_filtering`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`report`	`File`	`align_and_count.report`
`report_top_hits`	`File`	`align_and_count.report_top_hits`
`tophit`	`String`	`align_and_count.top_hit_id`
`pct_mapped_of_total_reads`	`String`	`align_and_count.pct_total_reads_mapped`
`pct_top_hit_of_total_reads`	`String`	`align_and_count.pct_top_hit_of_total_reads`
`pct_mapped_to_lesser_hits`	`String`	`align_and_count.pct_lesser_hits_of_mapped`
`viral_core_version`	`String`	`align_and_count.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `align_and_count` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 ~{docker}

~{docker}

Used by 1 task:

align_and_count

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flowchart TD
    Start([align_and_count_report])
    N1["align_and_count"]
    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_reports.wdl" as reports

workflow align_and_count_report {
    meta {
        description: "Align reads to reference with minimap2 and count the number of hits. Results are returned in the format of 'samtools idxstats'."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }
    parameter_meta {
        reads_unmapped_bams: {
            description: "Unaligned reads in BAM format",
            patterns: ["*.bam"]
        }
        ref_db: {
            description: "File containing sequences against which reads should me aligned and counted",
            patterns: ["*.fasta","*.fa"]
        }
    }

    call reports.align_and_count
    output {
        File   report                    = align_and_count.report
        File   report_top_hits           = align_and_count.report_top_hits
        String tophit                    = align_and_count.top_hit_id
        
        String pct_mapped_of_total_reads  = align_and_count.pct_total_reads_mapped
        String pct_top_hit_of_total_reads = align_and_count.pct_top_hit_of_total_reads
        String pct_mapped_to_lesser_hits  = align_and_count.pct_lesser_hits_of_mapped
        
        String viral_core_version        = align_and_count.viralngs_version
    }
}