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example.nf
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example.nf
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#!/usr/bin/env nextflow
params.ref = 'path/to/ref.fasta'
params.left = 'path/to/reads_1.fastq'
params.right = 'path/to/reads_2.fastq'
params.outdir = 'results'
// Create reference transcriptome index using Salmom
process salmonIndex {
input:
path ref from params.ref
output:
path index into txome_index
"""
salmon index -t '${ref}' -i index
"""
}
// Transcriptome alignment and quantification using Salmon
process salmonAlignQuant {
publishDir params.outdir
input:
path index from txome_index
path left from params.left
path right from params.right
output:
path 'quant'
"""
salmon quant -i $index -l A -1 '${left}' -2 '${right}' --validateMappings -o quant
"""
}
// FastQC
process fastQC {
publishDir params.outdir
input:
path index from txome_index
path left from params.left
path right from params.right
output:
path 'qc'
"""
mkdir qc && fastqc --quiet '${params.left}' '${params.right}' --outdir qc
"""
}