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Merge pull request #327 from nf-core/TCLamnidis-patch-2

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Removed all time limits
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James A. Fellows Yates 2022-02-10 10:22:53 +01:00 committed by GitHub
commit 192839c8be
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1 changed files with 0 additions and 23 deletions
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23
conf/pipeline/eager/eva.config
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@ -19,43 +19,36 @@ process {
withLabel:'sc_tiny'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'sc_small'{ withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'sc_medium'{ withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_small'{ withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) } cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_medium' { withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) } cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_large'{ withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) } cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_huge'{ withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) } 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 // 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'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.5.GB * task.attempt, 'memory' ) } 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'{ withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'sc_medium'{ withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_small'{ withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) } cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_medium' { withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) } cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_large'{ withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) } cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 24.GB * task.attempt, 'memory' ) } memory = { check_max( 24.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_huge'{ withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) } 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 // 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 { withName:hostremoval_input_fastq {
memory = { check_max( 32.GB * task.attempt, 'memory' ) } memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
} }
withName: maltextract { withName: maltextract {
@ -378,43 +363,36 @@ profiles {
withLabel:'sc_tiny'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) } memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'sc_small'{ withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'sc_medium'{ withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_small'{ withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) } cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_medium' { withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) } cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_large'{ withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) } cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) } memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
} }
withLabel:'mc_huge'{ withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 512.GB * task.attempt, 'memory' ) } 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 // 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 { withName:hostremoval_input_fastq {
memory = { check_max( 32.GB * task.attempt, 'memory' ) } memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
} }
withName: metagenomic_complexity_filter { withName: metagenomic_complexity_filter {