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nextflow.config
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/*
* -------------------------------------------------
* Predector Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
manifest {
name = 'predector'
author = 'Lina Rosano, Darcy Jones, James Hane'
homePage = 'https://github.com/ccdmb/predector'
doi = '10.1038/s41598-021-99363-0'
description = 'A pipeline to predict effectors.'
mainScript = 'main.nf'
nextflowVersion = '>=21'
version = '1.2.7'
}
// Global default params, used in configs
params {
proteome = false
phibase = false
pfam_hmm = false
pfam_dat = false
dbcan = false
effectordb = false
precomputed = false
precomputed_ldjson = false
chunk_size = 5000
nostrip = false
signalp6_bsize = 32
no_localizer = false
no_signalp6 = false
no_pfam = false
no_dbcan = false
no_phibase = false
no_effectordb = false
secreted_weight = 2
sigpep_good_weight = 0.003
sigpep_ok_weight = 0.0001
single_transmembrane_weight = -0.7
multiple_transmembrane_weight = -1.0
deeploc_extracellular_weight = 1.3
deeploc_intracellular_weight = -1.3
deeploc_membrane_weight = -0.25
targetp_mitochondrial_weight = -0.5
effectorp1_weight = 0.5
effectorp2_weight = 2.5
effectorp3_apoplastic_weight = 0.5
effectorp3_cytoplastmic_weight = 0.5
effectorp3_noneffector_weight = -2.5
deepredeff_fungi_weight = 0.1
deepredeff_oomycete_weight = 0.0
effector_homology_weight = 2
virulence_homology_weight = 0.5
lethal_homology_weight = -2
tmhmm_first60_threshold = 10
outdir = 'results'
symlink = false
help = false
license = false
version = false
tracedir = "${params.outdir}/pipeline_info"
// Things below this aren't intended to be settable by user
pfam_targets = "${baseDir}/data/pfam_targets.txt"
dbcan_targets = "${baseDir}/data/dbcan_targets.txt"
private_phibase_version = "v4-13"
// The PHI-base team often rename files. Best to get a release from a commit rather than master.
private_phibase_url = "https://raw.githubusercontent.com/PHI-base/data/7e1ae98bed14ee709d4b3e08f09fe87a6368b842/releases/phi-base_4-13_2022-05-09.fas"
private_pfam_version = "35.0"
private_pfam_hmm_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/Pfam-A.hmm.gz"
private_pfam_dat_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/Pfam-A.hmm.dat.gz"
private_dbcan_version = "V11"
private_dbcan_url = "https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V11.txt"
private_effectordb_url = "https://figshare.com/ndownloader/files/31397770"
private_effectordb_version = "1"
}
// Load base.config by default for all pipelines
includeConfig "${baseDir}/conf/base.config"
includeConfig "${baseDir}/conf/c4.config"
includeConfig "${baseDir}/conf/r8.config"
process.container = "predector/predector:${manifest.version}"
profiles {
docker {
docker.enabled = true
}
docker_sudo {
docker.enabled = true
docker.sudo = true
}
podman {
podman.enabled = true
}
singularity {
singularity.enabled = true
}
test {
includeConfig "$baseDir/conf/test.config"
}
pawsey_zeus {
includeConfig "${baseDir}/conf/c16.config"
includeConfig "${baseDir}/conf/r64.config"
includeConfig "${baseDir}/conf/t1.config"
includeConfig "$baseDir/conf/pawsey_zeus.config"
}
c4 {
includeConfig "${baseDir}/conf/c4.config"
}
c8 {
includeConfig "${baseDir}/conf/c8.config"
}
c16 {
includeConfig "${baseDir}/conf/c16.config"
}
r4 {
includeConfig "${baseDir}/conf/r4.config"
}
r6 {
includeConfig "${baseDir}/conf/r6.config"
}
r8 {
includeConfig "${baseDir}/conf/r8.config"
}
r16 {
includeConfig "${baseDir}/conf/r16.config"
}
r32 {
includeConfig "${baseDir}/conf/r32.config"
}
r64 {
includeConfig "${baseDir}/conf/r64.config"
}
t1 {
includeConfig "${baseDir}/conf/t1.config"
}
t2 {
includeConfig "${baseDir}/conf/t2.config"
}
t3 {
includeConfig "${baseDir}/conf/t3.config"
}
t4 {
includeConfig "${baseDir}/conf/t4.config"
}
c4r16 {
includeConfig "${baseDir}/conf/c4.config"
includeConfig "${baseDir}/conf/r16.config"
}
c4r16 {
includeConfig "${baseDir}/conf/c4.config"
includeConfig "${baseDir}/conf/r16.config"
}
c8r16 {
includeConfig "${baseDir}/conf/c8.config"
includeConfig "${baseDir}/conf/r16.config"
}
c8r32 {
includeConfig "${baseDir}/conf/c8.config"
includeConfig "${baseDir}/conf/r32.config"
}
c16r32 {
includeConfig "${baseDir}/conf/c16.config"
includeConfig "${baseDir}/conf/r32.config"
}
c16r64 {
includeConfig "${baseDir}/conf/c16.config"
includeConfig "${baseDir}/conf/r64.config"
}
}
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
podman.runOptions = '-u \$(id -u):\$(id -g)'
// Mount the filesystem with singularity.
singularity.autoMounts = true
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
file = "${params.tracedir}/pipeline_dag.svg"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}