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main.nf
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#!/usr/bin/env nextflow
/*
#==============================================
code documentation
#==============================================
*/
/*
#==============================================
params
#==============================================
*/
params.resultsDir = 'results/snippy'
params.filePattern = "./*_{R1,R2}.fastq.gz"
params.saveMode = 'copy'
params.ram = 4
params.cpus = 4
params.snippyCore = false
params.refGbk = "NC000962_3.gbk"
Channel.fromFilePairs(params.filePattern)
.set { ch_in_snippy }
Channel.value("$workflow.launchDir/NC000962_3.gbk")
.set { ch_refGbk }
/*
#==============================================
snippy
#==============================================
*/
process snippy {
container 'quay.io/biocontainers/snippy:4.6.0--0'
publishDir params.resultsDir, mode: params.saveMode
stageInMode 'symlink'
errorStrategy 'retry'
maxRetries 3
input:
path refGbk from ch_refGbk
set genomeFileName, file(genomeReads) from ch_in_snippy
output:
path("""${genomeName}""") into ch_out_snippy
when:
!params.snippyCore
script:
genomeName = genomeFileName.toString().split("\\_")[0]
"""
snippy --cpus ${params.cpus} --ram ${params.ram} --outdir $genomeName --ref $refGbk --R1 ${genomeReads[0]} --R2 ${genomeReads[1]}
"""
}
// TODO implement the snippy-core process
process snippyCore {
container 'ummidock/snippy_tseemann:4.6.0-02'
publishDir params.resultsDir, mode: params.saveBy
when:
params.snippyCore
input:
path refGbk from ch_refGbk
set genomeFileName, file(genomeReads) from ch_in_snippy
output:
path("""${genomeName}""") into ch_out_snippy
script:
"""
snippy-core
"""
}
/*
#==============================================
# extra
#==============================================
*/
// alternative container
//container 'ummidock/snippy_tseemann:4.6.0-02'