quick and dirty assembly with dragonflye

dragonflye.nf

#!/usr/bin/env nextflow

params.inputDir = "./fastq/*.fastq.gz"
params.outdir = "./results"

Channel
	.fromPath(params.inputDir).map { tuple (it.name.split('.fastq.gz')[0], it ) }
	.set { fastq_assemble_ch }

process dragonflye {

    publishDir "${params.outdir}", mode: 'copy', pattern: "${sample_id}_dragonflye_out/contigs.fa"
    publishDir "${params.outdir}", mode: 'copy', pattern: "${sample_id}_dragonflye_out/flye-info.txt"
    
    input:
    set val(sample_id),path(reads) from fastq_assemble_ch
    
    output:
    path "${sample_id}_dragonflye_out/contigs.fa" into assembly_ch
    path "${sample_id}_dragonflye_out/flye-info.txt" into assembly_info_ch
    
    script:
    """
    dragonflye --reads $reads --outdir ${sample_id}_dragonflye_out --cpus ${task.cpus} --medaka 3 --model r941_min_fast_g303
    """
}

nextflow.config

process {
    withName:dragonflye{
      container = 'quay.io/biocontainers/dragonflye:1.0.2--hdfd78af_0'
      cpus = 12
      clusterOptions = "-S /bin/bash -cwd -l mf=16G"
    }

    executor = 'sge'
    penv = 'smp'
    queue = 'global.q'
    errorStrategy = 'retry'
    maxRetries = 1

}

docker {
    enabled = false
}

singularity {
    enabled = true
    autoMounts = true
}