process SEQKIT_SPLIT2 { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("**/*.gz"), emit: reads path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if(meta.single_end){ """ seqkit \\ split2 \\ $args \\ --threads $task.cpus \\ $reads \\ --out-dir ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } else { """ seqkit \\ split2 \\ $args \\ --threads $task.cpus \\ --read1 ${reads[0]} \\ --read2 ${reads[1]} \\ --out-dir ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } }