From 3db7f0642a25d12eb942dafdfe60b6cc5db64964 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 15 Mar 2021 14:38:54 -0500 Subject: [PATCH] feat(appyter): Add initial module Co-authored-by: sruthipsuresh --- software/appyter/functions.nf | 59 +++++++++++++++++++++++++++++++++++ software/appyter/main.nf | 37 ++++++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 software/appyter/functions.nf create mode 100644 software/appyter/main.nf diff --git a/software/appyter/functions.nf b/software/appyter/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/appyter/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/appyter/main.nf b/software/appyter/main.nf new file mode 100644 index 00000000..ba7ffab6 --- /dev/null +++ b/software/appyter/main.nf @@ -0,0 +1,37 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process APPYTER { + tag "$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 + """ +}