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eva.config
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eva.config
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params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs'
}
env {
OPENBLAS_NUM_THREADS=1
OMP_NUM_THREADS=1
}
process {
errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
time = 365.d
withName: FASTQC {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withLabel:process_single {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = 365.d
}
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = 365.d
}
withLabel:process_medium {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = 365.d
}
withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = 365.d
}
withLabel:process_long {
time = 365.d
}
withLabel:process_high_memory {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
time = 365.d
}
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
withName: BOWTIE2_HOST_REMOVAL_BUILD {
cpus = { check_max (10 * task.attempt, 'cpus' ) }
memory = { check_max (20.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: BOWTIE2_HOST_REMOVAL_ALIGN {
cpus = { check_max (10 * task.attempt, 'cpus' ) }
memory = { check_max (10.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
cpus = { check_max (4 * task.attempt, 'cpus' ) }
memory = { check_max (8.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: PORECHOP {
cpus = { check_max (4 * task.attempt, 'cpus' ) }
memory = { check_max (30.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: NANOLYSE {
cpus = { check_max (2 * task.attempt, 'cpus' ) }
memory = { check_max (10.GB * task.attempt, 'memory' ) }
time = 365.d
}
//filtlong: exponential increase of memory and time with attempts
withName: FILTLONG {
cpus = { check_max (8 * task.attempt , 'cpus' ) }
memory = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
time = 365.d
}
withName: CENTRIFUGE {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (40.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: KRAKEN2 {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (40.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: KRONA {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (20.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: CAT_DB_GENERATE {
memory = { check_max (200.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: CAT {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (40.GB * task.attempt, 'memory' ) }
time = 365.d
}
withName: GTDBTK_CLASSIFYWF {
cpus = { check_max (10 * task.attempt, 'cpus' ) }
memory = { check_max (128.GB * task.attempt, 'memory' ) }
time = 365.d
}
//MEGAHIT returns exit code 250 when running out of memory
withName: MEGAHIT {
cpus = { check_megahit_cpus (8, task.attempt ) }
memory = { check_max (40.GB * task.attempt, 'memory' ) }
time = 365.d
errorStrategy = { task.exitStatus in ((130..145) + 104 + 250) ? 'retry' : 'finish' }
}
//SPAdes returns error(1) if it runs out of memory (and for other reasons as well...)!
//exponential increase of memory and time with attempts, keep number of threads to enable reproducibility
withName: SPADES {
cpus = { check_spades_cpus (10, task.attempt) }
memory = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
time = 365.d
errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
maxRetries = 5
}
withName: SPADESHYBRID {
cpus = { check_spadeshybrid_cpus (10, task.attempt) }
memory = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
maxRetries = 5
}
//returns exit code 247 when running out of memory
withName: BOWTIE2_ASSEMBLY_ALIGN {
cpus = { check_max (2 * task.attempt, 'cpus' ) }
memory = { check_max (8.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
}
withName: METABAT2_METABAT2 {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (20.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
}
withName: MAG_DEPTHS {
memory = { check_max (16.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
}
withName: BUSCO {
cpus = { check_max (8 * task.attempt, 'cpus' ) }
memory = { check_max (20.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
}
withName: MAXBIN2 {
// often fails when insufficient information, so we allow it to gracefully fail without failing the pipeline
errorStrategy = { task.exitStatus in [ 1, 255 ] ? 'ignore' : 'retry' }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
}
withName: DASTOOL_DASTOOL {
// if SCGs not found, bins cannot be assigned and DAS_tool will die with exit status 1
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
time = { check_max (24.h * (2**(task.attempt-1)), 'time' ) }
}
}