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Tweak eager settigs

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This commit is contained in:
James Fellows Yates 2022-03-03 14:29:30 +01:00
parent 18890fc3cf
commit 70318c3b2a
2 changed files with 103 additions and 99 deletions
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196
conf/pipeline/eager/mpcdf.config
View file

@ -1,119 +1,121 @@
// 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 MPCDF profile provided by nf-core/configs'
}
profile {
cobra {
// Specific nf-core/eager process configuration
process {
cobra {
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager MPCDF cobra profile provided by nf-core/configs'
}
process {
withName: malt {
maxRetries = 1
memory = 725.GB
cpus = 40
time = 24.h
}
withName: malt {
maxRetries = 1
memory = 725.GB
cpus = 40
time = 24.h
}
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = 24.h
}
}
}
}
raven {
// Specific nf-core/eager process configuration
process {
raven {
// Specific nf-core/eager process configuration
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager MPCDF raven profile provided by nf-core/configs'
}
process {
withName: malt {
maxRetries = 1
memory = 2048.GB
cpus = 72
time = 24.h
}
withName: malt {
maxRetries = 1
memory = 20000000.MB
cpus = 72
time = 24.h
}
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_huge'{
cpus = { check_max( 72, 'cpus' ) }
memory = { check_max( 240.GB * task.attempt, 'memory' ) }
time = 24.h
}
withLabel:'mc_huge'{
cpus = { check_max( 72, 'cpus' ) }
memory = { check_max( 240.GB * task.attempt, 'memory' ) }
time = 24.h
}
}
}
}
}

2
docs/mpcdf.md
View file

@ -42,6 +42,8 @@ Sets the following parameters:
We offer a pipeline specific profile optimised for [nf-core/eager](https://nf-co.re/eager)
- Maximum parallel running jobs: 30
### nf-core/rnaseq
We offer a pipeline specific profile optimised for [nf-core/rnaseq](https://nf-co.re/rnaseq)