mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
593 lines
22 KiB
Text
593 lines
22 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"'
|
|
|
|
maxRetries = 2
|
|
|
|
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
|
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
|
|
|
|
withLabel:'sc_tiny'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'sc_small'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'sc_medium'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'mc_small'{
|
|
cpus = { check_max( 2, 'cpus' ) }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'mc_medium' {
|
|
cpus = { check_max( 4, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'mc_large'{
|
|
cpus = { check_max( 8, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
withLabel:'mc_huge'{
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
|
|
time = '365.d'
|
|
}
|
|
|
|
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
|
|
|
|
withName: makeSeqDict {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc_after_clipping {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: adapter_removal {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: bwa {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
|
|
}
|
|
|
|
withName: bwamem {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
|
|
}
|
|
|
|
withName: bowtie2 {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
|
|
}
|
|
|
|
withName: samtools_flagstat {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: samtools_flagstat_after_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: dedup {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: markduplicates {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
memory = { check_max( 20.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: seqtype_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: additional_library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: metagenomic_complexity_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
}
|
|
|
|
withName: malt {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: maltextract {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: multivcfanalyzer {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: mtnucratio {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: vcf2genome {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: qualimap {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
|
}
|
|
|
|
withName: damageprofiler {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circulargenerator {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: preseq {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
|
}
|
|
|
|
withName: genotyping_ug {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName:get_software_versions {
|
|
cache = false
|
|
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
|
|
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName:eigenstrat_snp_coverage {
|
|
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
|
|
}
|
|
|
|
withName:kraken_merge {
|
|
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
|
|
}
|
|
|
|
withName:multiqc {
|
|
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
|
|
}
|
|
}
|
|
|
|
profiles {
|
|
|
|
medium_data {
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
|
config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs'
|
|
}
|
|
|
|
executor {
|
|
queueSize = 8
|
|
}
|
|
|
|
process {
|
|
|
|
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
|
|
|
|
maxRetries = 2
|
|
|
|
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
|
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
|
|
|
|
withLabel:'sc_tiny'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'sc_small'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'sc_medium'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_small'{
|
|
cpus = { check_max( 2, 'cpus' ) }
|
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_medium' {
|
|
cpus = { check_max( 4, 'cpus' ) }
|
|
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_large'{
|
|
cpus = { check_max( 8, 'cpus' ) }
|
|
memory = { check_max( 24.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_huge'{
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
// Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use
|
|
|
|
withName: makeSeqDict {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc_after_clipping {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: adapter_removal {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: samtools_flagstat {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
}
|
|
|
|
withName: samtools_flagstat_after_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
}
|
|
|
|
withName: dedup {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: markduplicates {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
}
|
|
|
|
withName: seqtype_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
}
|
|
|
|
withName: additional_library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: metagenomic_complexity_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
}
|
|
|
|
withName: malt {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName:hostremoval_input_fastq {
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: maltextract {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: multivcfanalyzer {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: mtnucratio {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: vcf2genome {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: qualimap {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
|
}
|
|
|
|
withName: damageprofiler {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circulargenerator {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: genotyping_ug {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: preseq {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
|
}
|
|
}
|
|
}
|
|
|
|
big_data {
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
|
config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
|
|
}
|
|
|
|
executor {
|
|
queueSize = 6
|
|
}
|
|
|
|
process {
|
|
|
|
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
|
|
|
|
maxRetries = 2
|
|
|
|
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
|
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
|
|
|
|
withLabel:'sc_tiny'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'sc_small'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'sc_medium'{
|
|
cpus = { check_max( 1, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_small'{
|
|
cpus = { check_max( 2, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_medium' {
|
|
cpus = { check_max( 4, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_large'{
|
|
cpus = { check_max( 8, 'cpus' ) }
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withLabel:'mc_huge'{
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 512.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
|
|
|
|
withName: makeSeqDict {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: fastqc_after_clipping {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: adapter_removal {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: samtools_flagstat {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: samtools_flagstat_after_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: dedup {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: markduplicates {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
memory = { check_max( 48.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: seqtype_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: additional_library_merge {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName:hostremoval_input_fastq {
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: metagenomic_complexity_filter {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: malt {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: maltextract {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: multivcfanalyzer {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: mtnucratio {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: vcf2genome {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: qualimap {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
|
}
|
|
|
|
withName: damageprofiler {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: circulargenerator {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: genotyping_ug {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
}
|
|
|
|
withName: preseq {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
|
}
|
|
}
|
|
}
|
|
|
|
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
|
|
}
|
|
}
|
|
}
|