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nextflow.config
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nextflow.config
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/*
To run with docker or singularity, use command line:
nextflow run main_stampy.nf -profile test_docker
nextflow run main_bwa.nf -profile test_docker
*/
manifest {
description = 'Oxford MMM CompassCompact Pipelines'
author = 'Oxford MMM team'
}
singularity {
enabled = true
}
executor {
queueSize = 10000
}
process {
withLabel: clockwork {
container = '/data/images/clockwork_container-0.7.7.img'
}
withLabel: fatos {
container = '/data/images/fatos-1.7.img'
}
withLabel: compass {
container = '/data/images/oxfordmmm_compasscompact_v1.0.2.img'
}
errorStrategy = 'ignore'
}
profiles {
standard {
process{
errorStrategy = 'ignore' //If the process return error, try it up to maxErrors
maxErrors = 1
}
env {
COMPASSCFG = "/home/compass/PIPELINE/compass/lib/compass.cfg"
SYS_ROOT = "/home/compass/PIPELINE"
COMPASS_ROOT= "$SYS_ROOT/compass"
SAMTOOL1x = "$SYS_ROOT/gorm-tools/samtools-1.4.1"
JAVA7="/opt/java17/bin"
PICARD = "$SYS_ROOT/gorm-tools/picard-tools-1.123"
BWA = "$SYS_ROOT/gorm-tools/bwa-0.7.15"
}
}
test_docker {
process{
container = 'oxfordmmm/compasscompact:v1.0.2'
errorStrategy = 'retry' //If the process return error, try it up to maxErrors
maxErrors = 1
}
docker {
enabled = true
runOptions = '-v /home/docker/Code/CompassCompact/docker/compass:/home/compass/PIPELINE/compass'
}
env {
COMPASSCFG = "/home/compass/PIPELINE/compass/lib/compass.cfg"
SYS_ROOT = "/home/compass/PIPELINE"
COMPASS_ROOT= "$SYS_ROOT/compass"
SAMTOOL1x = "$SYS_ROOT/gorm-tools/samtools-1.4.1"
JAVA7="/opt/java17/bin"
PICARD = "$SYS_ROOT/gorm-tools/picard-tools-1.123"
BWA = "$SYS_ROOT/gorm-tools/bwa-0.7.15"
}
}
}