Newer
Older
/*
* -------------------------------------------------
* nf-core/hic Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
// Global default params, used in configs
params {
// Workflow flags
input = "data/*{1,2}.fastq.gz"
genome = false
readPaths = false
chromosome_size = false
restriction_fragments = false
skip_maps = false
skip_ice = false
skip_cool = false
skip_multiqc = false
save_reference = false
save_interaction_bam = false
save_aligned_intermediates = false
rm_dup = false
rm_singleton = false
rm_multi = false
min_restriction_fragment_size = false
max_restriction_fragment_size = false
min_insert_size = false
max_insert_size = false
min_cis_dist = false
// Boilerplate options
name = false
email = false
email_on_fail = false
max_multiqc_email_size = 25.MB
plaintext_email = false
igenomes_base = 's3://ngi-igenomes/igenomes/'
tracedir = "${params.outdir}/pipeline_info"
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
// Defaults only, expecting to be overwritten
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
profiles {
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
}
test { includeConfig 'conf/test.config' }
}
// Load igenomes.config if required
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
}
report {
enabled = true
}
trace {
enabled = true
}
dag {
enabled = true
}
manifest {
name = 'nf-core/hic'
author = 'Nicolas Servant'
homePage = 'https://github.com/nf-core/hic'
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}