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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
#==============================================
code documentation
#==============================================
*/
/*
#==============================================
params
#==============================================
*/
params.index = false
params.faidx = false
params.sort = false
params.depth = false
params.gatkMarkDuplicatesSparkResultsDir = 'results/gatk/markDuplicatesSpark'
params.bwaMemResultsDir = 'results/bwa/mem'
params.faidxResultsDir = 'results/samtools/faidx'
params.sortResultsDir = 'results/samtools/sort'
params.indexResultsDir = 'results/samtools/index'
params.depthResultsDir = 'results/samtools/depth'
params.saveMode = 'copy'
params.refFasta = "NC000962_3.fasta"
params.readsFilePattern = "./*_{R1,R2}.fastq.gz"
params.bamFilePattern = ".bam"
params.sortedBamFilePattern = ".sort.bam"
Channel.value("$workflow.launchDir/$params.refFasta")
.set { ch_refFasta }
Channel.fromFilePairs(params.readsFilePattern)
.set { ch_in_samtools }
Channel.fromPath("${params.bwaMemResultsDir}/*${params.bamFilePattern}")
.set { ch_in_sort }
Channel.fromPath("${params.gatkMarkDuplicatesSparkResultsDir}/*${params.sortedBamFilePattern}")
.into { ch_in_index; ch_in_depth }
/*
#==============================================
faidx
#==============================================
*/
process faidx {
publishDir params.faidxResultsDir, mode: params.saveMode
container 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
when:
params.faidx
input:
path refFasta from ch_refFasta
output:
file('*.fai') into ch_out_faidx
script:
"""
samtools faidx $params.refFasta
"""
}
/*
#==============================================
sort
#==============================================
*/
process sort {
publishDir params.sortResultsDir, mode: params.saveMode
container 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
when:
params.sort
input:
file(bamRead) from ch_in_sort
output:
file("*${params.sortedBamFilePattern}") into ch_out_sort
script:
genomeName = bamRead.toString().split("\\.")[0]
"""
samtools sort ${bamRead} > ${genomeName}.sort.bam
"""
}
/*
#==============================================
index
#==============================================
*/
process index {
publishDir params.indexResultsDir, mode: params.saveMode
container 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
when:
params.index
input:
path refFasta from ch_refFasta
file(sortedBam) from ch_in_index
output:
file("*.bai") into ch_out_index
script:
"""
samtools index ${sortedBam}
"""
}
/*
#==============================================
depth
#==============================================
*/
process depth {
publishDir params.depthResultsDir, mode: params.saveMode
container 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
when:
params.depth
input:
path refFasta from ch_refFasta
file(sortedBam) from ch_in_depth
output:
file("*.txt") into ch_out_depth
script:
genomeName = sortedBam.toString().split("\\.")[0]
"""
samtools depth ${sortedBam} > ${genomeName}_depth_out.txt
"""
}
/*
#==============================================
# extra
#==============================================
*/