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60 lines
1.9 KiB
Text
60 lines
1.9 KiB
Text
/*
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* -------------------------------------------------
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* Nextflow config file for running tests
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* -------------------------------------------------
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* Defines bundled input files and everything required
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* to run a fast and simple test. Use as follows:
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* nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
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*/
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params {
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config_profile_name = 'nf-core/eager nucleaer - human profile'
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config_profile_description = "A simple profile for human nuclear genomes"
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email = 'pluisi@pasteur.fr'
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}
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process {
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errorStrategy = 'retry'
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maxRetries = 2
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withName:'makeBWAIndex'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'adapter_removal'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'bwa'{
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cpus = { check_max( 15 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName:'markduplicates'{
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'damageprofiler'{
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cpus = 1
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastp'{
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cpus = 8
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastqc'{
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cpus = 2
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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