nf-core_modules/software/hisat2/build/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
def VERSION = '2.2.0'
process HISAT2_BUILD {
tag "$fasta"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::hisat2=2.2.0=py37hfa133b6_4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
} else {
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
}
input:
path fasta
path gtf
path splicesites
output:
path "hisat2", emit: index
path "*.version.txt", emit: version
script:
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 extract_exons = ''
def ss = ''
def exon = ''
if (avail_mem > params.hisat_build_memory) {
log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in 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 ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
}
def software = getSoftwareName(task.process)
"""
mkdir hisat2
$extract_exons
hisat2-build \\
-p $task.cpus \\
$ss \\
$exon \\
$options.args \\
$fasta \\
hisat2/${fasta.baseName}
echo $VERSION > ${software}.version.txt
"""
}