process GENESCOPEFK { tag "$meta.id" label 'process_low' if (params.enable_conda) { error "Conda environments cannot be used when using the GeneScope tool. Please use docker or singularity containers." } container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0' input: tuple val(meta), path(fastk_histex_histogram) output: tuple val(meta), path("*_linear_plot.png") , emit: linear_plot tuple val(meta), path("*_log_plot.png") , emit: log_plot tuple val(meta), path("*_model.txt") , emit: model tuple val(meta), path("*_summary.txt") , emit: summary tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // Git commit id is used instead of GeneScopeFK.R -v as software is not release versioned. """ GeneScopeFK.R \\ $args \\ --input $fastk_histex_histogram \\ --output . \\ --name_prefix ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": genescope: $GENESCOPE_VERSION r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' ) END_VERSIONS """ }