def VERSION = '2.2.0' // Version information not provided by tool on CLI process HISAT2_BUILD { tag "$fasta" label 'process_high' label 'process_high_memory' conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) container "${ 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 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." } """ 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 """ }