From cd8bacc90a7c40755455542b7151679db9c2c691 Mon Sep 17 00:00:00 2001 From: Ravneet Bhuller Date: Mon, 5 Jul 2021 10:17:57 +0100 Subject: [PATCH] PR for lofreq/indelqual module (#539) * first commit * edited functions.nf * edited functions.nf * version line updated * Update software/lofreq/indelqual/main.nf Co-authored-by: Harshil Patel * Update software/lofreq/indelqual/main.nf Co-authored-by: Harshil Patel * Update software/lofreq/indelqual/main.nf Co-authored-by: Harshil Patel * Update software/lofreq/indelqual/meta.yml Co-authored-by: Harshil Patel * Update tests/software/lofreq/indelqual/test.yml Co-authored-by: Harshil Patel * Update tests/software/lofreq/indelqual/main.nf Co-authored-by: Harshil Patel * updated files * updated file Co-authored-by: Harshil Patel --- software/lofreq/indelqual/functions.nf | 68 ++++++++++++++++++++++++ software/lofreq/indelqual/main.nf | 40 ++++++++++++++ software/lofreq/indelqual/meta.yml | 44 +++++++++++++++ tests/config/pytest_software.yml | 4 ++ tests/software/lofreq/indelqual/main.nf | 16 ++++++ tests/software/lofreq/indelqual/test.yml | 8 +++ 6 files changed, 180 insertions(+) create mode 100644 software/lofreq/indelqual/functions.nf create mode 100644 software/lofreq/indelqual/main.nf create mode 100644 software/lofreq/indelqual/meta.yml create mode 100644 tests/software/lofreq/indelqual/main.nf create mode 100644 tests/software/lofreq/indelqual/test.yml diff --git a/software/lofreq/indelqual/functions.nf b/software/lofreq/indelqual/functions.nf new file mode 100644 index 00000000..da9da093 --- /dev/null +++ b/software/lofreq/indelqual/functions.nf @@ -0,0 +1,68 @@ +// +// Utility functions used in nf-core DSL2 module files +// + +// +// Extract name of software tool from process name using $task.process +// +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] + } + path = path instanceof String ? path : '' + path_list.add(path) + } + } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/lofreq/indelqual/main.nf b/software/lofreq/indelqual/main.nf new file mode 100644 index 00000000..befd8d7a --- /dev/null +++ b/software/lofreq/indelqual/main.nf @@ -0,0 +1,40 @@ +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process LOFREQ_INDELQUAL { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4" + } else { + container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4" + } + + input: + tuple val(meta), path(bam) + path fasta + + output: + tuple val(meta), path("*.bam"), emit: bam + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + lofreq indelqual \\ + $options.args \\ + -f $fasta \\ + -o ${prefix}.bam \\ + $bam + + echo \$(lofreq version 2>&1) | sed 's/^.*lofreq //; s/Using.*\$//' > ${software}.version.txt + """ +} diff --git a/software/lofreq/indelqual/meta.yml b/software/lofreq/indelqual/meta.yml new file mode 100644 index 00000000..294cf17d --- /dev/null +++ b/software/lofreq/indelqual/meta.yml @@ -0,0 +1,44 @@ +name: lofreq_indelqual +description: Inserts indel qualities in a BAM file +keywords: + - bam + - indel + - qualities +tools: + - lofreq: + description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file + homepage: https://csb5.github.io/lofreq/ + doi: "10.1093/nar/gks918" + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - bam: + type: file + description: BAM file with indel qualities inserted into it + pattern: "*.{bam}" + +authors: + - "@kaurravneet4123" diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index c514b1fa..2dffe1b1 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -422,6 +422,10 @@ last/train: - software/last/train/** - tests/software/last/train/** +lofreq/indelqual: + - software/lofreq/indelqual/** + - tests/software/lofreq/indelqual/** + mash/sketch: - software/mash/sketch/** - tests/software/mash/sketch/** diff --git a/tests/software/lofreq/indelqual/main.nf b/tests/software/lofreq/indelqual/main.nf new file mode 100644 index 00000000..8dd76029 --- /dev/null +++ b/tests/software/lofreq/indelqual/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + + +include { LOFREQ_INDELQUAL } from '../../../../software/lofreq/indelqual/main.nf' addParams( options: [ 'args': '--dindel', 'suffix':'.indelqual'] ) + +workflow test_lofreq_indelqual { + + input = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + + LOFREQ_INDELQUAL ( input, fasta ) +} diff --git a/tests/software/lofreq/indelqual/test.yml b/tests/software/lofreq/indelqual/test.yml new file mode 100644 index 00000000..769e4b04 --- /dev/null +++ b/tests/software/lofreq/indelqual/test.yml @@ -0,0 +1,8 @@ +- name: lofreq indelqual + command: nextflow run ./tests/software/lofreq/indelqual -entry test_lofreq_indelqual -c tests/config/nextflow.config + tags: + - lofreq + - lofreq/indelqual + files: + - path: output/lofreq/test.indelqual.bam + md5sum: 18de975638c2633069bfe1a41ebc5ff7