Merge pull request #146 from heuermh/bandage

Add bandage image module
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Kevin Menden 2021-02-05 08:00:44 +01:00 committed by GitHub
commit 17dd0415f2
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7 changed files with 1625 additions and 0 deletions

4
.github/filters.yml vendored
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bandage_image:
- software/bandage/image/**
- tests/software/bandage/image/**
bowtie_align: bowtie_align:
- software/bowtie/align/** - software/bowtie/align/**
- software/bowtie/build/** - software/bowtie/build/**

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/*
* -----------------------------------------------------
* 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"
}
}
}

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BANDAGE_IMAGE {
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), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2"
} else {
container "quay.io/biocontainers/bandage:0.8.1--hc9558a2_2"
}
input:
tuple val(meta), path(gfa)
output:
tuple val(meta), path('*.png'), emit: png
tuple val(meta), path('*.svg'), emit: svg
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
Bandage image $gfa ${prefix}.png $options.args
Bandage image $gfa ${prefix}.svg $options.args
echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
"""
}

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name: bandage_image
description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
keywords:
- gfa
- graph
- assembly
- visualisation
tools:
- bandage:
description: |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
homepage: https://github.com/rrwick/Bandage
documentation: https://github.com/rrwick/Bandage
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gfa:
type: file
description: Assembly graph in GFA 1.0 format
pattern: "*.gfa"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- png:
type: file
description: Bandage image in PNG format
pattern: "*.png"
- svg:
type: file
description: Bandage image in SVG format
pattern: "*.svg"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@heuermh"

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tests/data/gfa/B-3106.gfa Normal file

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BANDAGE_IMAGE } from '../../../../software/bandage/image/main.nf' addParams( options: [:] )
workflow test_bandage_image {
def input = []
input = [ [ id:'B-3106' ], // meta map
[ file("${launchDir}/tests/data/gfa/B-3106.gfa", checkIfExists: true) ] ]
BANDAGE_IMAGE ( input )
}

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- name: bandage image
command: nextflow run ./tests/software/bandage/image -entry test_bandage_image -c tests/config/nextflow.config
tags:
- bandage
- bandage_image
files:
- path: output/bandage/B-3106.png
- path: output/bandage/B-3106.svg