bio-workflow-management-wdl-workflows

Version Compatibility

Reference examples tested with: BWA 0.7.17+, FastQC 0.12+, GATK 4.5+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

WDL Workflows

"Build a WDL pipeline for Terra/AnVIL execution" → Define tasks and workflows in WDL (Workflow Description Language) for execution on Cromwell, miniwdl, or cloud platforms (Terra, AnVIL) with built-in GATK best practices support.

• CLI: cromwell run workflow.wdl or miniwdl run workflow.wdl for execution
• WDL: version 1.0 task/workflow syntax with scatter-gather parallelism

Basic Task Definition

version 1.0

task fastqc {
    input {
        File fastq
        Int threads = 2
    }

    command <<<
        fastqc -t ~{threads} ~{fastq}
    >>>

    output {
        File html = glob("*_fastqc.html")[0]
        File zip = glob("*_fastqc.zip")[0]
    }

    runtime {
        docker: "biocontainers/fastqc:v0.11.9"
        cpu: threads
        memory: "4 GB"
    }
}

Simple Workflow

version 1.0

workflow rnaseq {
    input {
        File fastq_1
        File fastq_2
        File salmon_index
    }

    call fastp {
        input:
            reads_1 = fastq_1,
            reads_2 = fastq_2
    }

    call salmon_quant {
        input:
            reads_1 = fastp.trimmed_1,
            reads_2 = fastp.trimmed_2,
            index = salmon_index
    }

    output {
        File quant_sf = salmon_quant.quant_file
    }
}

Task with All Sections

version 1.0

task bwa_mem {
    input {
        File reference
        File reference_index
        File reads_1
        File reads_2
        String sample_id
        Int threads = 8
    }

    Int disk_size = ceil(size(reference, "GB") + size(reads_1, "GB") * 3) + 20

    command <<<
        bwa mem -t ~{threads} -R "@RG\tID:~{sample_id}\tSM:~{sample_id}" \
            ~{reference} ~{reads_1} ~{reads_2} | \
            samtools sort -@ ~{threads} -o ~{sample_id}.sorted.bam
        samtools index ~{sample_id}.sorted.bam
    >>>

    output {
        File bam = "~{sample_id}.sorted.bam"
        File bai = "~{sample_id}.sorted.bam.bai"
    }

    runtime {
        docker: "biocontainers/bwa:v0.7.17"
        cpu: threads
        memory: "16 GB"
        disks: "local-disk " + disk_size + " HDD"
    }
}