mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
64 lines
2.3 KiB
Text
64 lines
2.3 KiB
Text
process HISAT2_BUILD {
|
|
tag "$fasta"
|
|
label 'process_high'
|
|
label 'process_high_memory'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
|
|
'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }"
|
|
|
|
input:
|
|
path fasta
|
|
path gtf
|
|
path splicesites
|
|
|
|
output:
|
|
path "hisat2" , emit: index
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def avail_mem = 0
|
|
if (!task.memory) {
|
|
log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
|
|
} else {
|
|
log.info "[HISAT2 index build] Available memory: ${task.memory}"
|
|
avail_mem = task.memory.toGiga()
|
|
}
|
|
|
|
def ss = ''
|
|
def exon = ''
|
|
def extract_exons = ''
|
|
def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as nextflow.util.MemoryUnit).toGiga() : 0
|
|
if (avail_mem >= hisat2_build_memory) {
|
|
log.info "[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index"
|
|
extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
|
|
ss = "--ss $splicesites"
|
|
exon = "--exon ${gtf.baseName}.exons.txt"
|
|
} else {
|
|
log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
|
|
log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
|
|
}
|
|
def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
mkdir hisat2
|
|
$extract_exons
|
|
hisat2-build \\
|
|
-p $task.cpus \\
|
|
$ss \\
|
|
$exon \\
|
|
$args \\
|
|
$fasta \\
|
|
hisat2/${fasta.baseName}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
hisat2: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|