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nextflow.config
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nextflow.config
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// Base configuration for the NGS pipelines
params {
verbose = true
// path to data
resourceDir = '/home/holtgrem/Data'
// path to genome to use
params.genome = "${resourceDir}/references/grch37/human_g1k_v37.fasta"
// path to indices to use
params.indexBWA = "${resourceDir}/indices/grch37-bwa/human_g1k_v37.fasta"
params.indexSTAR = "${resourceDir}/indices/grch37-star"
// path to exon BED files to use
params.exonsUCSC = "${resourceDir}/exons/grch37-ucsc/UCSC_exons_plus_10bp.bed.gz"
params.exonsCCDS = "${resourceDir}/exons/grch37-ccds/CCDS_exons_plus_10bp.bed.gz"
// threads / CPU usage
fastqc {
cpus = 2
}
// Configuration for Skewer.
skewer {
cpus = 8
// Adapters for left (parameter -x) and right (-y) reads.
adaptersR1 = "${resourceDir}/adapters/TruSeq3-PE-R1.fa"
adaptersR2 = "${resourceDir}/adapters/TruSeq3-PE-R2.fa"
}
// Configuration of BWA mapping (includes piped samtools called)
bwa {
cpus = 8
}
// Configuration of STAR mapping
star {
cpus = 8
}
// Configuration of Freebayes calling
freebayes {
cpus = 8
}
}