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nextflow.config
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params {
dataDir = "${PWD}/data"
// Model to use during taxonomy classification
// More pre-trained models at https://docs.qiime2.org/2019.7/data-resources/
classifier = "https://data.qiime2.org/2019.7/common/gg-13-8-99-515-806-nb-classifier.qza"
prefix = "" // project prefix to prepend to output files
outdir = "out" // output directory
// Parameters required by QIIME2
truncF = null
truncR = null
samplingDepth = null
// Extra QIIME2 parameters
demuxExtra = ""
demuxSumExtra = ""
denoiseExtra = ""
phylogenyExtra = ""
taxonomyClassificationExtra = ""
visualizeDenoiseStatsExtra = ""
visualizeTaxonomyExtra = ""
}
manifest {
homePage = 'https://github.com/Liulab/ubiome'
author = 'Ha Le, Jake Carlson'
description = 'Microbiome analysis workflow with QIIME2'
version = '0.1'
nextflowVersion = '>=19.07.0'
}
profiles {
standard {
process.conda = "${baseDir}/environment.yml"
}
docker {
process.container = 'haqle/qiime2-nextflow:2019.7'
docker.enabled = true
}
singularity {
process.container = 'haqle/qiime2-nextflow:2019.7'
singularity.enabled = true
}
slurm {
process.executor = 'slurm'
process.memory = '4GB'
process.time = '12h'
process.scratch = true
}
}