Use optional workflow inputs as non optional input for task

Hi,

I have a workflow with an optional input that needs to be used in task where the same input is not optional.

example

version 1.0

task PicardCollectHsMetrics {
    meta {
        description: "Collects hybrid-selection (HS) metrics for a SAM or BAM file."
    }

    input {
        File input_bam
        File bait_intervals_bed
        File target_intervals_bed

        FastaReference reference_fasta

        String docker_image = "quay.io/biocontainers/gatk4:4.1.9.0--py39_0"
    }

    String input_bam_basename = basename(input_bam, ".bam")
    String bait_name = basename(bait_intervals_bed, ".bed")

    command {
        set -e

        # bait regions
        gatk BedToIntervalList \
            -I ~{target_intervals_bed} \
            -O target.interval_list \
            -SD ~{reference_fasta.ref_dict}

        # target regions
        gatk BedToIntervalList \
            -I ~{bait_intervals_bed} \
            -O bait.interval_list \
            -SD ~{reference_fasta.ref_dict}

        gatk CollectHsMetrics \
            -I ~{input_bam} \
            -O ~{input_bam_basename}_hs_metrics.txt \
            -R ~{reference_fasta.ref_fasta} \
            -N ~{bait_name} \
            -BAIT_INTERVALS bait.interval_list \
            -TARGET_INTERVALS target.interval_list
    }

    runtime {
        docker: docker_image
        cpu: 1
        maxRetries: 2
    }

    output {
        File hs_metrics = "~{input_bam_basename}_hs_metrics.txt"
    }
}


task PicardCollectWgsMetrics {
    meta {
        description: "Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments."
    }

    input {
        File input_bam

        FastaReference reference_fasta

        String docker_image = "quay.io/biocontainers/gatk4:4.1.9.0--py39_0"
    }

    String input_bam_basename = basename(input_bam, ".bam")

    command {
        set -e
        gatk CollectWgsMetrics \
            -I ~{input_bam} \
            -O ~{input_bam_basename}_wgs_metrics.txt \
            -R ~{reference_fasta.ref_fasta}
    }

    runtime {
        docker: docker_image
        cpu: 1
        maxRetries: 2
    }

    output {
        File wgs_metrics = "~{input_bam_basename}_wgs_metrics.txt"
    }
}


workflow Metrics {
    input {
        File input_bam
        File? bait_intervals_bed
        File? target_intervals_bed
        FastaReference reference_fasta
    }

    if (defined(bait_intervals_bed) && defined(target_intervals_bed)) {
        call PicardCollectHsMetrics {
            input:
                input_bam  = MergeSortMarkDupBams.output_bam,
                bait_intervals_bed = bait_intervals_bed,
                target_intervals_bed = target_intervals_bed,
                reference_fasta = bwa_reference.reference_fasta
        }
    }
    if (!defined(bait_intervals_bed) && !defined(target_intervals_bed)) {
        call qc.PicardCollectWgsMetrics {
            input:
                input_bam  = MergeSortMarkDupBams.output_bam,
                reference_fasta = bwa_reference.reference_fasta
        }
    }
}

...

How do I accomplish such a thing? womtool says Cannot coerce expression of type 'File?' to 'File'.

Thanks for the help. Matthias

[pshapiro4broad]

I think you get the behavior you want by not using select_first(). If you have an optional value, and you’re passing it to a workflow that accepts an optional value, then you can pass it directly. You only need to use select_first() if you’re passing an optional value to a workflow that accepts a non-optional value.

[mlin]

Yea everybody learning WDL gets tripped up by this at some point. I have made (future versions of) miniwdl suggest select_first() on this type error.