mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 17:19:54 +00:00
219 lines
7.4 KiB
Text
219 lines
7.4 KiB
Text
// Profile config names for nf-core/configs
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
|
config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
|
|
}
|
|
|
|
// Specific nf-core/eager process configuration
|
|
process {
|
|
|
|
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
|
|
|
|
maxRetries = 2
|
|
|
|
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
|
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
|
|
|
|
withLabel:'sc_tiny'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'sc_small'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'sc_medium'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_small'{
|
|
cpus = { check_max( 2, 'cpus' ) }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_medium' {
|
|
cpus = { check_max( 4, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_large'{
|
|
cpus = { check_max( 8, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_huge'{
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
|
|
|
|
withName: makeSeqDict {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: fastqc {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: adapter_removal {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: dedup {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: markduplicates {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
|
|
}
|
|
|
|
withName: library_merge {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
|
|
}
|
|
|
|
withName: malt {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: maltextract {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: multivcfanalyzer {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: mtnucratio {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: vcf2genome {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: qualimap {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
|
|
}
|
|
|
|
withName: damageprofiler {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: circulargenerator {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: preseq {
|
|
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
|
}
|
|
|
|
}
|
|
|
|
profiles {
|
|
|
|
big_data {
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
|
config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
|
|
}
|
|
|
|
executor {
|
|
queueSize = 6
|
|
}
|
|
|
|
process {
|
|
|
|
maxRetries = 2
|
|
|
|
withName:hostremoval_input_fastq {
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
time = 1440.h
|
|
}
|
|
|
|
withLabel:'sc_tiny'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'sc_small'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'sc_medium'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_small'{
|
|
cpus = { check_max( 2, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_medium' {
|
|
cpus = { check_max( 4, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_large'{
|
|
cpus = { check_max( 8, 'cpus' ) }
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
|
|
withLabel:'mc_huge'{
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 512.GB * task.attempt, 'memory' ) }
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
|
|
}
|
|
}
|
|
}
|
|
|
|
pathogen_loose {
|
|
params {
|
|
config_profile_description = 'Pathogen (loose) MPI-EVA profile, provided by nf-core/configs.'
|
|
bwaalnn = 0.01
|
|
bwaalnl = 16
|
|
}
|
|
}
|
|
pathogen_strict {
|
|
params {
|
|
config_profile_description = 'Pathogen (strict) MPI-EVA SDAG profile, provided by nf-core/configs.'
|
|
bwaalnn = 0.1
|
|
bwaalnl = 32
|
|
}
|
|
}
|
|
human {
|
|
params {
|
|
config_profile_description = 'Human MPI-EVA SDAG profile, provided by nf-core/configs.'
|
|
bwaalnn = 0.01
|
|
bwaalnl = 16500
|
|
}
|
|
}
|
|
}
|