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added unlimitedtime profile to maestro; changed cache for bwa process

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pierrespc 2021-10-08 09:05:46 +02:00
parent 1621585558
commit 035ab61f61
2 changed files with 22 additions and 9 deletions
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22
conf/pipeline/eager/maestro.config
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@ -2,14 +2,14 @@
* ------------------------------------------------- * -------------------------------------------------
* Nextflow config file for running nf-core eager on whole genome data or mitogenomes * Nextflow config file for running nf-core eager on whole genome data or mitogenomes
* ------------------------------------------------- * -------------------------------------------------
* nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear or mitocondrial) * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
*/ */
params { params {
config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles' config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
config_profile_description = "Simple profiles for human nuclear or mito genomes" config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "
} }
@ -32,15 +32,16 @@ profiles {
time = { check_max( 12.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withName:'bwa'{ withName:'bwa'{
cpus = { check_max( 30 * task.attempt, 'cpus' ) } cpus = { check_max( 40 * task.attempt, 'cpus' ) }
memory = { check_max( 40.GB * task.attempt, 'memory' ) } memory = { check_max( 40.GB * task.attempt, 'memory' ) }
time = 24.h time = 24.h
cache = 'deep'
} }
withName:'markduplicates'{ withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withName:'damageprofiler'{ withName:'damageprofiler'{
cpus = 1 cpus = 1
@ -103,4 +104,13 @@ profiles {
} }
} }
} }
unlimitedtime {
process {
errorStrategy = 'finish'
cpus = 5
memory = 200.GB
time = 8760.h
}
} }

9
docs/pipeline/eager/maestro.md
View file

@ -14,8 +14,7 @@ Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear`
Specific configurations for maestro has been made for eager. Specific configurations for maestro has been made for eager.
We decided not to provide any Tool parameter here and focus the profile only for ressource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos so increasing the memnory and CPUs, specially for alignments). We decided not to provide any tool parameters here, and focus the profile only for resource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos, so increasing the memory and CPUs, specially for alignments).
## nuclear ## nuclear
@ -24,6 +23,10 @@ Increases the number of CPUs and the amount of memory for key processes
##mitochondrial ##mitochondrial
more limited computational ressources More limited computational resources
##unlimitedtime
Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles.
Expect slow processes when using this profile because only 5 CPUs are available at a time.