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nextflow.config
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nextflow.config
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manifest {
name = 'telatin/getreads'
author = 'Andrea Telatin'
homePage = 'https://github.com/telatin/getreads'
description = 'A Small SRA downloader Pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '2.2'
}
params {
outdir = "getreads"
tracedir = "${params.outdir}/pipeline_info"
// Defaults only, expecting to be overwritten
max_memory = '16.GB'
max_cpus = 8
max_time = '12.h'
}
process {
// TODO nf-core: Check the defaults for all processes
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = {
task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish'
}
maxRetries = 1
maxErrors = '-1'
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 5
}
}
profiles {
conda {
conda.enabled = true
params.enable_conda = true
process.conda = "$baseDir/deps/env2.yaml"
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
process.container = 'andreatelatin/getreads:3.0'
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
process.container = 'docker://andreatelatin/getreads:3.0'
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
test {
params.list = "$baseDir/test/list.txt"
params.outdir = "$baseDir/test/output"
max_memory = '4.GB'
max_cpus = 1
max_time = '24.h'
process {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}