task with_bias_correction {
    Int bootstrap_count
    File fastq_zipfile
    String kallisto_index_name
    File kallisto_index_file
    Int frag_length_mean
    Int frag_length_sd

    command <<<
        source activate kallisto-env
        kallisto quant \
            --index=${kallisto_index_file} \
            --fusion \
            --bias \
            --threads 2 \
            --output-dir . \
            --single \
            --fragment-length=${frag_length_mean} \
            --sd=${frag_length_sd} \
            --bootstrap-samples=${bootstrap_count} \
            ${fastq_zipfile}
    >>>

    output {
        String index_used = kallisto_index_name
        File abundance = "abundance.tsv"
        File bootstraps = "abundance.h5"
        File run_info = "run_info.json"
        File fusion = "fusion.txt"
    }

    runtime {
        disks: "local-disk 75 HDD"
        cpu: 2
        memory: "7 GB"
        docker: "vanallenlab/kallisto:kallisto-v0.43.1-latest"
        preemptible: 1
    }
}

task no_bias_correction {
    Int bootstrap_count
    File fastq_zipfile
    String kallisto_index_name
    File kallisto_index_file
	Int frag_length_mean
    Int frag_length_sd

    command <<<
        source activate kallisto-env
        kallisto quant \
            --index=${kallisto_index_file} \
            --fusion \
            --threads 2 \
            --output-dir . \
            --single \
            --fragment-length=${frag_length_mean} \
            --sd=${frag_length_sd} \
            --bootstrap-samples=${bootstrap_count} \
            ${fastq_zipfile}
    >>>

    output {
        String index_used = kallisto_index_name
        File abundance = "abundance.tsv"
        File bootstraps = "abundance.h5"
        File run_info = "run_info.json"
        File fusion = "fusion.txt"
    }

    runtime {
        disks: "local-disk 75 HDD"
        cpu: 2
        memory: "7 GB"
        docker: "vanallenlab/kallisto:kallisto-v0.43.1-latest"
        preemptible: 1
    }
}

workflow kallisto_quant {
    Int bootstrap_count
    File fastq_zipfile
    String kallisto_index_name
    File kallisto_index_file
    Int frag_length_mean
    Int frag_length_sd

    call with_bias_correction {
        input:
            bootstrap_count=bootstrap_count,
            fastq_zipfile=fastq_zipfile,
            kallisto_index_name=kallisto_index_name,
            kallisto_index_file=kallisto_index_file,
            frag_length_mean=frag_length_mean,
            frag_length_sd=frag_length_sd
    }

    call no_bias_correction {
        input:
            bootstrap_count=bootstrap_count,
            fastq_zipfile=fastq_zipfile,
            kallisto_index_name=kallisto_index_name,
            kallisto_index_file=kallisto_index_file,
            frag_length_mean=frag_length_mean,
            frag_length_sd=frag_length_sd
    }
}