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nextflow.config
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nextflow.config
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// Select multiple profiles by using -profile local, singularity
profiles {
local {
params.location='local'
process.executor='local'
}
slurm {
params.location='slurm'
process.executor='slurm'
process.queue='high'
}
conda {
params.pkm = 'conda'
params.rootdir = '/tmp/jasen/'
params.outdir = "${params.rootdir}/results/"
params.assets = "${params.rootdir}/assets/"
params.reference = "${params.assets}/test_data/references/AP017922.1.fasta"
params.krakendb="${params.assets}/references/minikraken2/"
params.aribadb="${params.assets}/references/ariba/"
params.chewbbacadb="${params.assets}/references/chewbbaca/"
}
singularity {
params.pkm = 'singularity'
params.rootdir ="/out/"
params.work = "${params.rootdir}/scratch/"
env.NXF_WORK="${params.work}"
env.NXF_TEMP="${params.work}"
env.NXF_SINGULARITY_LOCALCACHEDIR="${params.work}"
env.NXF_SINGULARITY_CACHEDIR="${params.work}"
env.NXF_SINGULARITY_TMPDIR="${params.work}"
env.SINGULARITY_LOCALCACHEDIR="${params.work}"
env.SINGULARITY_CACHEDIR="${params.work}"
env.SINGULARITY_TMPDIR="${params.work}"
env.SINGULARITY_ROOTFS="${params.work}"
env.TMPDIR="${params.work}"
env.TEMPDIR="${params.work}"
params.outdir = "${params.rootdir}/results/"
params.assets = "${params.rootdir}/assets/"
params.reference = "${params.assets}/test_data/references/AP017922.1.fasta"
params.krakendb="${params.assets}/references/minikraken2/"
params.aribadb="${params.assets}/references/ariba/"
params.chewbbacadb="${params.assets}/references/chewbbaca/"
singularity.enabled = true
singularity.runOptions = "-B ${baseDir}:/external -B /scratch/tmp/:/out -e -W ${params.work} --pwd ${params.work} --env-file /JASEN/container/environment.yml"
singularity.autoMounts = true
}
}
params {
krakendb_url="ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/16S_Silva138_20200326.tgz"
chewbbacadb_url="https://www.cgmlst.org/ncs/schema/3887469/alleles/"
ariba_db_download = true
chewbbaca_db_download = true
kraken_db_download = true
input = "${baseDir}/assets/test_data/sequencing_data/saureus_100k"
adapters = "${baseDir}/assets/test_data/adapters/NexteraPE-PE.fa"
prodigal_file="${baseDir}/assets/prodigal_training_files/Enterococcus_faecium.trn"
}
process {
withLable: min_allocation {
cpus = 1
memory = '2.GB'
time = '15m'
}
withLabel: modest_allocation {
cpus = 1
memory = '4.GB'
time = '1h'
}
withLabel: max_allocation {
cpus = 1
memory = '6.GB'
time = '2h'
}
}
manifest {
name = 'genomic-medicine-sweden/JASEN'
author = 'Isak Sylvin et al.'
homePage = 'https://github.com/genomic-medicine-sweden/JASEN.git'
description = 'Json producing Assembly driven microbial Sequence analysis pipeline to support Epitypification and Normalize classification decisions'
mainScript = 'main.nf'
nextflowVersion = '>=10.0.0'
version = '0.1.0'
}