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nextflow.config
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72 lines (61 loc) · 1.51 KB
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// Global default parameters
params {
outdir = 'annotater'
fasta = null // fasta sequences to annotate
config = null // annotater configuration file
evalue = null // evalue cutoff (i.e. 1e-5)
qc = null // query coverage cutoff (i.e. 50)
pid = null // percent identity cutoff (i.e. 80)
// Taxonomy params
tax = false // run taxonomy (if without -remotetax must set the below local taxonomy options)
remotetax = false // only do remote taxonomy (must also set -tax)
// Local taxonomy params
taxasql = null
namesdmp = null
nodesdmp = null
pipeline_outdir = "./results"
pipeline_info = "./results/pipeline_info"
}
process {
withName: ANNOTATER {
cpus = 4
time = 24.h
}
}
profiles {
docker {
docker.enabled = true
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}
report {
overwrite = true
enabled = true
file = "${params.pipeline_info}/report.html"
}
timeline {
overwrite = true
enabled = true
file = "${params.pipeline_info}/timeline.html"
}
trace {
overwrite = true
enabled = true
file = "${params.pipeline_info}/trace.txt"
}
dag {
overwrite = true
enabled = true
file = "${params.pipeline_info}/flowchart.dot"
// file = "${params.pipeline_info}/flowchart.png" //requires graphviz for rendering
}
manifest {
name = 'pcantalupo/annotater'
author = 'Paul Cantalupo'
description = 'Annotation of fasta sequences'
mainScript = 'main.nf'
version = '1.0.2'
}