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