From 42188eec6f763a32d4ea440f52bc7f95028efd11 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Wed, 25 Oct 2023 15:09:55 +0200 Subject: [PATCH 1/2] Add picard_addorreplacereadgroups sge memory overhead --- conf/pipeline/eager/eva.config | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 8376719f6..abb183398 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -188,6 +188,10 @@ process { 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' } @@ -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' } @@ -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' } From ae9809319351134a0d4dba605a13816270af9975 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Wed, 25 Oct 2023 15:11:50 +0200 Subject: [PATCH 2/2] make whitespace consistent --- conf/pipeline/eager/eva.config | 96 +++++++++++++++++----------------- 1 file changed, 48 insertions(+), 48 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index abb183398..02ee6e26d 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -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=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } @@ -111,91 +111,91 @@ process { withName: dedup { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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 @@ -222,7 +222,7 @@ profiles { executor { queueSize = 8 - } + } process { @@ -309,16 +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" } @@ -329,7 +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' ) } @@ -402,7 +402,7 @@ profiles { executor { queueSize = 6 - } + } process { @@ -437,14 +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 @@ -490,16 +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=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } - } + } withName:hostremoval_input_fastq { memory = { check_max( 32.GB * task.attempt, 'memory' ) } @@ -514,7 +514,7 @@ profiles { cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } - } + } withName: maltextract { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } @@ -585,13 +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 - } + } } }