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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
#==============================================
code documentation
#==============================================
*/
/*
#==============================================
PARAMS
#==============================================
*/
/*
#----------------------------------------------
flags
#----------------------------------------------
*/
params.FLAG = false
/*
#----------------------------------------------
directories
#----------------------------------------------
*/
params.resultsDir = 'results/FIXME'
/*
#----------------------------------------------
file patterns
#----------------------------------------------
*/
params.refFasta = "NC000962_3.fasta"
params.readsFilePattern = "./*_{R1,R2}.fastq.gz"
/*
#----------------------------------------------
misc
#----------------------------------------------
*/
params.saveMode = 'copy'
/*
#----------------------------------------------
channels
#----------------------------------------------
*/
Channel.value("$workflow.launchDir/$params.refFasta")
.set { ch_refFasta }
Channel.fromFilePairs(params.readsFilePattern)
.set { ch_in_PROCESS }
/*
#==============================================
PROCESS
#==============================================
*/
process PROCESS {
publishDir params.resultsDir, mode: params.saveMode
container 'FIXME'
input:
set genomeFileName, file(genomeReads) from ch_in_PROCESS
output:
path FIXME into ch_out_PROCESS
script:
genomeName = genomeFileName.toString().split("\\_")[0]
"""
CLI PROCESS
"""
}
/*
#==============================================
# extra
#==============================================
*/