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nextflow.config
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nextflow.config
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env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
manifest {
mainScript = 'main.nf'
}
includeConfig "$baseDir/params.config"
process {
containerOptions = { workflow.containerEngine == "docker" ? '-e USER=$USER -e HOME=$HOME -u $(id -u):$(id -g)': null}
queue = 'long-sl7,short-sl7'
cache = 'lenient'
memory='4.5G'
cpus='1'
time='6h'
scratch = false
containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
withLabel: big_cpus {
cpus = 2
memory = '5G'
}
withLabel: incr_time_cpus {
errorStrategy = 'retry'
memory = '5G'
cpus = 2
time = {6.h * task.attempt * task.attempt}
maxRetries = 4
}
withLabel: big_mem {
cpus = 1
memory = '5G'
}
withLabel: big_mem_retry {
errorStrategy = 'retry'
memory = {5.GB * task.attempt}
cpus = 1
maxRetries = 4
}
}
process.container = 'biocorecrg/exon_intron_pipe:0.2'
//singularity.enabled = true
singularity.cacheDir = "$baseDir/singularity"
// Modify accordig to cloud parameters
profiles {
awsbatch {
process.executor = 'awsbatch'
process.queue = 'spot'
workDir = 's3://data-nf/work'
aws.region = 'eu-central-1'
aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
singularity.enabled = false
docker.enabled = true
}
}