diff_genome_sets
pipes/WDL/workflows/diff_genome_sets.wdl

WORKFLOW diff_genome_sets

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

Imports

Namespace Path
reports ../tasks/tasks_reports.wdl
utils ../tasks/tasks_utils.wdl

Workflow: diff_genome_sets

Inputs

Name Type Description Default
genome_set_one Array[File] - -
genome_set_two Array[File] - -
2 optional inputs with default values

Outputs

Name Type Expression
diff File tsv_stack.out_tsv

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS compare_two_genomes ↗

Input Mappings (3)
Input Value
genome_one sample.left
genome_two sample.right
out_basename basename(sample.left,'.fasta')

CALL TASKS tsv_stack ↗

Input Mappings (2)
Input Value
input_tsvs compare_two_genomes.comparison_table
out_basename "diff_genome_sets"

Images

Container images used by tasks in this workflow:

🐳 ~{docker}

~{docker}

Used by 1 task:
  • tsv_stack
🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • compare_two_genomes
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diff_genome_sets - Workflow Graph

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diff_genome_sets - WDL Source Code

version 1.0

import "../tasks/tasks_reports.wdl" as reports
import "../tasks/tasks_utils.wdl" as utils

workflow diff_genome_sets {

    input {
        Array[File]   genome_set_one
        Array[File]   genome_set_two
    }

    scatter(sample in zip(genome_set_one, genome_set_two)) {
        call reports.compare_two_genomes {
            input:
                genome_one   = sample.left,
                genome_two   = sample.right,
                out_basename = basename(sample.left, '.fasta')
        }
    }

    call utils.tsv_stack {
        input:
            input_tsvs   = compare_two_genomes.comparison_table,
            out_basename = "diff_genome_sets"
    }

    output {
        File diff = tsv_stack.out_tsv
    }

}