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Merge pull request #578 from nf-core/update_eva_eager_config
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Update eva eager config
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@TCLamnidis
TCLamnidis authored Oct 25, 2023
2 parents 1d084d6 + ae98093 commit 3ac12c5
Showing 1 changed file with 59 additions and 47 deletions.
106 changes: 59 additions & 47 deletions conf/pipeline/eager/eva.config
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Original file line number Diff line number Diff line change
Expand Up @@ -51,38 +51,38 @@ process {
}

withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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' ) }
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=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
Expand Down Expand Up @@ -111,87 +111,91 @@ process {
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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 {
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 {
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: picard_addorreplacereadgroups {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
}

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
Expand All @@ -218,7 +222,7 @@ profiles {

executor {
queueSize = 8
}
}

process {

Expand Down Expand Up @@ -305,16 +309,16 @@ profiles {

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 {
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" }
Expand All @@ -325,7 +329,7 @@ profiles {
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' ) }
Expand Down Expand Up @@ -372,6 +376,10 @@ profiles {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}

withName: picard_addorreplacereadgroups {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}

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' }
Expand All @@ -394,7 +402,7 @@ profiles {

executor {
queueSize = 6
}
}

process {

Expand Down Expand Up @@ -429,14 +437,14 @@ profiles {
}

withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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' ) }
}
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

Expand Down Expand Up @@ -482,16 +490,16 @@ profiles {
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 {
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' ) }
Expand All @@ -506,7 +514,7 @@ profiles {
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" }
Expand Down Expand Up @@ -549,6 +557,10 @@ profiles {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}

withName: picard_addorreplacereadgroups {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
}

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' }
Expand All @@ -573,13 +585,13 @@ profiles {
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
}
}
}
}

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