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donut_falls_template.config
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donut_falls_template.config
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//# Docker Params -------------------------------------------
//docker.enabled = true
//docker.runOptions = '-u \$(id -u):\$(id -g)'
//docker.sudo = false
//docker.temp = /tmp
//docker.remove = true
//docker.registry = ''
//docker.fixOwnership = true
//docker.engineOptions = ''
//docker.mountFlags = ''
//# Singularity Params --------------------------------------
//singularity.enabled = true
//singularity.autoMounts = true
//singularity.runOptions = ""
//process.stageInMode = "link"
//singularity.engineOptions = ''
//singularity.cacheDir = ''
//# AWS Batch Params ----------------------------------------
//process.executor = 'awsbatch'
//process.queue = ''
//aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
//aws.region = 'us-east-1'
//workDir = 's3://'
//# Google Cloud Params -------------------------------------
//process.executor = ''
//google.project = ''
//google.location = ''
//google.region = ''
//workDir = ''
//google.lifeSciences.bootDiskSize = 50.GB
//# Nextflow Tower ------------------------------------------
//tower.accessToken = ''
//tower.enabled = true
//# Adjustable Workflow paramters ---------------------------
//# specifies input files
//# header = sample,fastq,fastq_1,fastq_2
//# sample = value for filenames
//# fastq = nanopore fastq file
//# fastq_1 = optional: illumina R1 fastq file
//# fastq_2 = optional: illumina R2 fastq file
//params.sample_sheet = ''
//# specifies assembler to use. Options are 'flye', 'raven', and 'unicycler' in any combination
//# examples:
//params.assembler = 'flye'
//params.assembler = 'unicycler'
//params.assembler = 'flye,raven'
//params.assembler = 'unicyclerraven'
//# when set to true, creates a copy of this template file for the end user
//params.config_file = false
//# directory where results are placed
//params.outdir = 'donut_falls'
//# adds test data to workflow
//params.test = false
//# runs nanoplot on nanopore sequencing summary
//params.sequencing_summary = ""
//# Getting reports for the run
// timeline {
// enabled = true
// }
// report {
// enabled = true
// }
// trace {
// enabled = true
// }
// dag {
// enabled = true
// }
//process {
//# final directory
// publishDir = [ path: params.outdir, mode: 'copy' ]
//
// maxRetries = 1
// maxErrors = '-1'
//
//# labels (groups of processes)
// withLabel:process_single {
// cpus = { 1 }
// memory = { 6.GB }
// time = { 10.m * task.attempt }
// }
// withLabel:process_low {
// cpus = { 2 }
// memory = { 12.GB }
// time = { 2.h * task.attempt }
// }
// withLabel:process_medium {
// cpus = { 6 }
// memory = { 36.GB }
// time = { 4.h * task.attempt }
// }
// withLabel:process_high {
// cpus = { 12 }
// memory = { 72.GB }
// time = { 16.h * task.attempt }
// }
// withLabel:process_long {
// time = { 20.h * task.attempt }
// }
// withLabel:process_high_memory {
// memory = { 200.GB * task.attempt }
// }
//
//# individual processes
// withName:bandage{
// label = 'process_low'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/bandage:0.8.1'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// time = '10m'
// ext.args = ''
// ext.prefix = '${gfa.baseName}'
// }
// withName:busco{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/busco:5.7.1-prok-bacteria_odb10_2024-01-08'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// time = '45m'
// ext.args = '--offline -l /busco_downloads/lineages/bacteria_odb10'
// ext.prefix = "${fasta.baseName}"
// }
// withName:bwa{
// label = 'process_high'
// // no publishDir
// container = 'staphb/bwa:0.7.17'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// time = "'2h'"
// ext.args = ''
// ext.prefix = "${fasta.baseName}"
// }
// withName:circulocov{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/circulocov:0.1.20240104'
// time = '1h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = '-a'
// ext.prefix = '${fasta.baseName}'
// }
// withName:copy{
// label = 'process_low'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// }
// withName:dnaapler{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/dnaapler:0.7.0'
// time = '1h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = '${fasta.baseName}'
// }
// withName:fastp{
// label = 'process_low'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/fastp:0.23.4'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.lrargs = '--qualified_quality_phred 12 --length_required 1000'
// ext.prefix = '${meta.id}'
// }
// withName:flye{
// label = 'process_high'
// "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/flye:2.9.3'
// time = '10h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.read_type = '--nano-hq'
// ext.prefix = "${meta.id}"
// }
// withName:gfastats{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy', pattern: 'gfastats/*'
// container = 'staphb/gfastats:1.3.6'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = "${gfa.baseName}"
// }
// withName:gfa_to_fasta{
// label = 'process_low'
// // no publishDir
// container = 'staphb/multiqc:1.19'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore' }"
// }
// withName:mash{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/mash:2.3'
// time = '30m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.ont_args = '-m 2 -c 20'
// ext.ill_args = '-m 2 -c 20'
// ext.short_re = "${illumina.join(' ')}"
// ext.prefix = "${meta.id}"
// }
// withName:medaka{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'ontresearch/medaka:v1.11.3'
// time = '30m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = "${fasta.baseName.replaceAll('_reoriented','')}"
// }
// withName:multiqc{
// label = 'process_low'
// publishDir = "${params.outdir}", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// }
// withName:nanoplot_summary{
// label = 'process_low'
// publishDir = "${params.outdir}/summary", mode: 'copy'
// container = 'staphb/nanoplot:1.42.0'
// time = '30m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// }
// withName:nanoplot{
// label = 'process_low'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/nanoplot:1.42.0'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = ''
// }
// withName:polypolish{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/polypolish:0.6.0'
// time = '45m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.filarg = ''
// ext.prefix = ''
// }
// withName:png{
// label = "process_single"
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '45m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = "${meta.id}"
// }
// withName:pypolca{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/pypolca:0.3.1'
// time = '30m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = '--careful'
// ext.prefix = ''
// }
// withName:rasusa{
// label = 'process_medium'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/rasusa:0.8.0'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = '--genome-size 5mb --coverage 150'
// ext.prefix = ''
// }
// withName:raven{
// label = 'process_high'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/raven:1.8.3'
// time = '10h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = '--polishing-rounds 2'
// ext.prefix = ''
// }
// withName:summary{
// label = 'process_single'
// publishDir = "${params.outdir}/summary", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// }
// withName:unicycler{
// label = 'process_high'
// publishDir = "${params.outdir}/${meta.id}", mode: 'copy'
// container = 'staphb/unicycler:0.5.0'
// time = '10h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// ext.args = ''
// ext.prefix = ''
// }
// withName:versions{
// label = 'process_single'
// publishDir = "${params.outdir}/summary", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '10m'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// }
// withName:test{
// label = 'process_single'
// publishDir = "${params.outdir}/test_files/", mode: 'copy'
// container = 'staphb/multiqc:1.19'
// time = '1h'
// errorStrategy = "{ task.attempt < 2 ? 'retry' : 'ignore'}"
// }
// }