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main.nf
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main.nf
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process MINIMAP2_ALIGN {
tag "$meta.id"
label 'process_medium'
// Note: the versions here need to match the versions used in the mulled container below and minimap2/index
conda "bioconda::minimap2=2.24 bioconda::samtools=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
'biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
input:
tuple val(meta), path(reads)
path reference
val bam_format
val cigar_paf_format
val cigar_bam
val bed_format
output:
tuple val(meta), path("*.paf"), optional: true, emit: paf
tuple val(meta), path("*.bam"), optional: true, emit: bam
tuple val(meta), path("*.bed"), optional: true, emit: bed
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def bam_output = reference.size() > 2.5e9 && bam_format ? "-a | samtools view -b -T ${reference} - > ${prefix}.bam" : reference.size() < 2.5e9 && bam_format ? "-a | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : bed_format ? "| paftools.js splice2bed - > ${prefix}.bed " : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
"""
minimap2 \\
$args \\
-t $task.cpus \\
"${reference ?: reads}" \\
"$reads" \\
$cigar_paf \\
$set_cigar_bam \\
$bam_output
cat <<-END_VERSIONS > versions.yml
"${task.process}":
minimap2: \$(minimap2 --version 2>&1)
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def bam_output = reference.size() > 2.5e9 && bam_format ? "-a | samtools view -b -T ${reference} - > ${prefix}.bam" : reference.size() < 2.5e9 && bam_format ? "-a | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
def extension = bam_format ? "bam" : bed_format ? "bed" : "paf"
"""
touch ${prefix}.${extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
minimap2: \$(minimap2 --version 2>&1)
END_VERSIONS
"""
}