nf-core_modules/modules/genescopefk/main.nf
2022-06-14 20:49:06 +02:00

42 lines
1.5 KiB
Text

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
"""
}