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nextflow.config
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nextflow.config
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nextflow.enable.dsl = 2
params {
input = null
library = null
outdir = 'results'
exp_name = 'crispin'
count_table = null
design_matrix = null
enable_conda = false
publish_dir_mode = "copy"
cutadapt {
adapters = '/opt2/TruSeq_and_nextera_adapters.consolidated.fa' // this is in the cutadapt container
minlen = 20
leadingquality = 10
trailingquality = 10
}
mageck {
run = true
}
drugz {
run = true
remove_genes = null
half_window_size = 500 // same as default in drugZ https://github.com/hart-lab/drugz/blob/eb15d34e4dd172965e618d5bb662c053066da799/drugz.py#L305-L306
}
bagel {
run = true
core_essential_genes = '/opt2/bagel-2.0-115/CEGv2.txt' // in Docker container
non_essential_genes = '/opt2/bagel-2.0-115/NEGv1.txt' // in Docker container
test_columns = null
}
}
includeConfig 'conf/base.config'
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.cacheDir = "/data/$USER/.singularity" // TODO this may be a different default on other (non biowulf) platforms