def VERSION = '2.2.0' // Version information not provided by tool on CLI process HISAT2_ALIGN { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' : 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' }" input: tuple val(meta), path(reads) path index path splicesites output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.log") , emit: summary tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq 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 strandedness = '' if (meta.strandedness == 'forward') { strandedness = meta.single_end ? '--rna-strandness F' : '--rna-strandness FR' } else if (meta.strandedness == 'reverse') { strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF' } def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" if (meta.single_end) { def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'` hisat2 \\ -x \$INDEX \\ -U $reads \\ $strandedness \\ --known-splicesite-infile $splicesites \\ --summary-file ${prefix}.hisat2.summary.log \\ --threads $task.cpus \\ $seq_center \\ $unaligned \\ $args \\ | samtools view -bS -F 4 -F 256 - > ${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": hisat2: $VERSION samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } else { def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'` hisat2 \\ -x \$INDEX \\ -1 ${reads[0]} \\ -2 ${reads[1]} \\ $strandedness \\ --known-splicesite-infile $splicesites \\ --summary-file ${prefix}.hisat2.summary.log \\ --threads $task.cpus \\ $seq_center \\ $unaligned \\ --no-mixed \\ --no-discordant \\ $args \\ | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam if [ -f ${prefix}.unmapped.fastq.1.gz ]; then mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz fi if [ -f ${prefix}.unmapped.fastq.2.gz ]; then mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz fi cat <<-END_VERSIONS > versions.yml "${task.process}": hisat2: $VERSION samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } }