nf-core_modules/software/appyter/main.nf
Edmund Miller 3db7f0642a
feat(appyter): Add initial module
Co-authored-by:  sruthipsuresh <sps180004@utdallas.edu>
2021-03-17 10:20:34 -05:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process APPYTER {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
// FIXME These rely on docker and won't work with conda
// conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "$options.appyter_image"
} else {
container "$options.appyter_image}"
}
input:
path input
output:
path "data/output.ipynb", emit: output_notebook
path "*.version.txt" , emit: version
script:
// Add soft-links to original FastQs for consistent naming in pipeline
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
"""
appyter nbconstruct -i $input -o data/output.ipynb
"""
}