diff --git a/conf/maestro.config b/conf/maestro.config index bf48c23..8815932 100644 --- a/conf/maestro.config +++ b/conf/maestro.config @@ -1,6 +1,6 @@ params { config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA' + config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/' config_profile_contact = 'Pierre Luisi (@pierrespc)' } diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config new file mode 100644 index 0000000..473eec3 --- /dev/null +++ b/conf/pipeline/eager/maestro.config @@ -0,0 +1,107 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running nf-core eager on whole genome data or mitogenomes + * ------------------------------------------------- + * nextflow run nf-core/eager -profile maestro,,maestro, (where is long or normal and is nuclear or mitocondrial) + */ + +params { + + config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles' + + config_profile_description = "Simple profiles for human nuclear or mito genomes" + + email = 'pluisi@pasteur.fr' +} + + +profiles { + + nuclear { + 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( 30 * task.attempt, 'cpus' ) } + memory = { check_max( 40.GB * task.attempt, 'memory' ) } + time = 24.h + } + withName:'markduplicates'{ + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'damageprofiler'{ + cpus = 1 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastp'{ + cpus = 8 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastqc'{ + cpus = 2 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + } + } + + mitocondrial { + 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' ) } + } + } + } +} diff --git a/conf/pipeline/eager/maestromitocondrial.config b/conf/pipeline/eager/maestromitocondrial.config deleted file mode 100644 index 62c6e4e..0000000 --- a/conf/pipeline/eager/maestromitocondrial.config +++ /dev/null @@ -1,58 +0,0 @@ -/* - * ------------------------------------------------- - * 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,,maestromitocondrial (where 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' ) } - } -} diff --git a/conf/pipeline/eager/maestronuclear.config b/conf/pipeline/eager/maestronuclear.config deleted file mode 100644 index 7ec6a9c..0000000 --- a/conf/pipeline/eager/maestronuclear.config +++ /dev/null @@ -1,58 +0,0 @@ -/* - * ------------------------------------------------- - * Nextflow config file for running nf-core eager on whole genome data - * ------------------------------------------------- - * nextflow run nf-core/eager -profile maestro,,maestronuclear (where is long or normal) - */ - -params { - - config_profile_name = 'nf-core/eager nucleaer - human profile' - - config_profile_description = "A simple profile for human nuclear genomes" - - 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( 15 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = 24.h - } - withName:'markduplicates'{ - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'damageprofiler'{ - cpus = 1 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'fastp'{ - cpus = 8 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'fastqc'{ - cpus = 2 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } -} diff --git a/docs/maestro.md b/docs/maestro.md index cda14f7..59daa80 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -4,7 +4,7 @@ If you are using TARS cluster, please refer to pasteur profile. This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core +Please refer to docs/pasteur.md for installing and running nf-core instructions. -Run the pipeline with `-profile maestro,` where qos is long or normal +Run the pipeline with -profile maestro, where qos is long or normal. diff --git a/pipeline/eager.config b/pipeline/eager.config index 5825bab..10dd990 100644 --- a/pipeline/eager.config +++ b/pipeline/eager.config @@ -11,6 +11,5 @@ profiles { mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } - maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" } - maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" } + maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" } }