diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index d436895..67c3b5a 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,43 +19,36 @@ process { 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 @@ -196,43 +189,36 @@ profiles { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.5.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( 6.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( 12.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( 6.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( 12.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( 24.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 (and also some samtools?!) using more memory than you tell it to use @@ -297,7 +283,6 @@ profiles { withName:hostremoval_input_fastq { memory = { check_max( 32.GB * task.attempt, 'memory' ) } - time = 1440.h } withName: maltextract { @@ -378,43 +363,36 @@ profiles { 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 } } // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use @@ -469,7 +447,6 @@ profiles { withName:hostremoval_input_fastq { memory = { check_max( 32.GB * task.attempt, 'memory' ) } - time = 1440.h } withName: metagenomic_complexity_filter {