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/*
* SAMtools :
* Imputs : bam files
* Output : bam files
*/
/* bams sorting */
params.bam = "$baseDir/data/bam/*.bam"
log.info "bams files : ${params.bam}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
.set { bam_files }
process sort_bam {
tag "$bam.baseName"
cpus 4
input:
file bam from bam_files
output:
file "*_sorted.bam" into sorted_bam_files
script:
"""
samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
"""
}
/* bams indexing */
params.bam = "$baseDir/data/bam/*.bam"
log.info "bams files : ${params.bam}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
.set { bam_files }
process index_bam {
tag "$bam.baseName"
input:
file bam from bam_files
output:
file "*bam*" into indexed_bam_file
script:
"""
samtools index ${bam}
"""
}
/* bams spliting */
params.bam = "$baseDir/data/bam/*.bam"
log.info "bams files : ${params.bam}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
.set { bam_files }
process split_bam {
tag "$bam.baseName"
cpus 2
input:
file bam from bam_files
output:
file "*_forward.bam*" into forward_bam_files
file "*_reverse.bam*" into reverse_bam_files
script:
"""
samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
"""
}
/* bams filtering */
params.bam = "$baseDir/data/bam/*.bam"
params.bed = "$baseDir/data/bam/*.bed"
log.info "bams files : ${params.bam}"
log.info "bed file : ${params.bed}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
.set { bam_files }
Channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
.set { bed_files }
process filter_bam {
tag "$bam.baseName"
cpus 4
input:
file bam from bam_files
file bed from bed_files
output:
file "*_filtered.bam*" into filtered_bam_files
script:
"""
samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
"""
}