From 352a48741f8aa9e349017033607291019c9575c3 Mon Sep 17 00:00:00 2001 From: Sruthi Suresh Date: Mon, 9 Nov 2020 19:07:34 -0600 Subject: [PATCH] updated test file and main.nf file --- software/bedtools/slopRefseq/functions.nf | 59 ------------------- software/bedtools/sloprefseq/main.nf | 4 +- software/bedtools/sloprefseq/test/main.nf | 9 ++- .../bedtools/sloprefseq/test/nextflow.config | 1 + software/bedtools/sloprefseq/test_main.nf | 19 ------ 5 files changed, 9 insertions(+), 83 deletions(-) delete mode 100644 software/bedtools/slopRefseq/functions.nf delete mode 100644 software/bedtools/sloprefseq/test_main.nf diff --git a/software/bedtools/slopRefseq/functions.nf b/software/bedtools/slopRefseq/functions.nf deleted file mode 100644 index 54dc8fe8..00000000 --- a/software/bedtools/slopRefseq/functions.nf +++ /dev/null @@ -1,59 +0,0 @@ -/* - * ----------------------------------------------------- - * 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)}/$args.filename" - } - } -} \ No newline at end of file diff --git a/software/bedtools/sloprefseq/main.nf b/software/bedtools/sloprefseq/main.nf index d8b4cb5f..dbaaa311 100644 --- a/software/bedtools/sloprefseq/main.nf +++ b/software/bedtools/sloprefseq/main.nf @@ -21,8 +21,8 @@ process BEDTOOLS_SLOPREFSEQ { } input: - path sizes tuple val(meta), path(beds) + path sizes output: tuple val(meta), path("*.sloprefseq.bed"), emit: bed @@ -33,7 +33,7 @@ process BEDTOOLS_SLOPREFSEQ { def beds_files = beds.sort() def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ - slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed + slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r ${params.downstream} > ${prefix}.sloprefseq.bed bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt """ } diff --git a/software/bedtools/sloprefseq/test/main.nf b/software/bedtools/sloprefseq/test/main.nf index 3637bf10..834c1add 100644 --- a/software/bedtools/sloprefseq/test/main.nf +++ b/software/bedtools/sloprefseq/test/main.nf @@ -10,10 +10,13 @@ include { BEDTOOLS_SLOPREFSEQ } from '../../sloprefseq/main.nf' addParams( optio workflow test_bed_file{ def input = [] input = [ [ id:'test', single_end:true ], - [ file("${baseDir}/input/A.bed", checkIfExists: true), - file("${baseDir}/input/genome.sizes", checkIfExists: true) ] ] + [ file("${baseDir}/input/A.bed", checkIfExists: true),] ] - BEDTOOLS_SLOPREFSEQ ( input, [ publish_dir:'test_bed_file' ] ) + BEDTOOLS_SLOPREFSEQ ( + input, + file("${baseDir}/input/genome.sizes", checkIfExists: true) + ) + } diff --git a/software/bedtools/sloprefseq/test/nextflow.config b/software/bedtools/sloprefseq/test/nextflow.config index 01af7cef..4ee101de 100644 --- a/software/bedtools/sloprefseq/test/nextflow.config +++ b/software/bedtools/sloprefseq/test/nextflow.config @@ -1,3 +1,4 @@ + params { outdir = "output/" publish_dir_mode = "copy" diff --git a/software/bedtools/sloprefseq/test_main.nf b/software/bedtools/sloprefseq/test_main.nf deleted file mode 100644 index b79b02a0..00000000 --- a/software/bedtools/sloprefseq/test_main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.preview.dsl = 2 -params.out_dir = "test_output" -params.upstream = 1 -params.downstream = 10 - -include BEDTOOLS_SLOPEREFSEQ from '../main.nf' params(params) - -// Define input channels -ch_input_1 = Channel.fromPath('./tests/data/bed/A.bed') -ch_input_2 = Channel.fromPath('./tests/data/bed/genome.sizes') - -def additional_params_map = [:] - -// Run the workflow -workflow { - BEDTOOLS_SLOPEREFSEQ(ch_input_1, ch_input_2, additional_params_map) -}