millironx/nf-configs
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edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet

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pierrespc 2021-09-29 13:47:35 +02:00
parent b71df6fe57
commit f6266879d6
3 changed files with 61 additions and 4 deletions
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58
conf/pipeline/eager/maestromitocondrial.config Normal file
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@ -0,0 +1,58 @@
/*
* -------------------------------------------------
* Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_
* -------------------------------------------------
* nextflow run nf-core/eager -profile maestro,<qos>,maestromitocondrial (where <qos> is long or normal)
*/
params {
config_profile_name = 'nf-core/eager mitrocondrial - human profile'
config_profile_description = "A simple profile for human mitogenomes"
email = 'pluisi@pasteur.fr'
}
process {
errorStrategy = 'retry'
maxRetries = 2
withName:'makeBWAIndex'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'adapter_removal'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'bwa'{
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = 24.h
}
withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastp'{
cpus = 8
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastqc'{
cpus = 2
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}

6
conf/pipeline/eager/maestronuclear.config
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@ -1,10 +1,8 @@
/* /*
* ------------------------------------------------- * -------------------------------------------------
* Nextflow config file for running tests * Nextflow config file for running nf-core eager on whole genome data
* ------------------------------------------------- * -------------------------------------------------
* Defines bundled input files and everything required * nextflow run nf-core/eager -profile maestro,<qos>,maestronuclear (where <qos> is long or normal)
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
*/ */
params { params {

1
pipeline/eager.config
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@ -12,4 +12,5 @@ profiles {
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" } maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" }
maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" }
} }