Merge pull request #221 from heuermh/seqwish

Add module for seqwish/induce
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Harshil Patel 2021-02-17 22:14:49 +00:00 committed by GitHub
commit ecd26b388d
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7 changed files with 208 additions and 0 deletions

4
.github/filters.yml vendored
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@ -229,6 +229,10 @@ seacr_callpeak:
- software/seacr/callpeak/** - software/seacr/callpeak/**
- tests/software/seacr/callpeak/** - tests/software/seacr/callpeak/**
seqwish_induce:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
star_align: star_align:
- software/star/align/** - software/star/align/**
- tests/software/star/align/** - tests/software/star/align/**

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@ -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"
}
}
}

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@ -0,0 +1,44 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
def VERSION = '0.4.1'
process SEQWISH_INDUCE {
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) }
conda (params.enable_conda ? "bioconda::seqwish=0.4.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0"
} else {
container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
}
input:
tuple val(meta), path(paf), path(fasta)
output:
tuple val(meta), path("*.gfa"), emit: gfa
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
seqwish \\
--threads $task.cpus \\
--paf-alns=$paf \\
--seqs=$fasta \\
--gfa=${prefix}.gfa \\
$options.args
echo $VERSION > ${software}.version.txt
"""
}

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@ -0,0 +1,67 @@
name: seqwish_induce
description: Induce a variation graph in GFA format from alignments in PAF format
keywords:
- induce
- paf
- gfa
- graph
- variation graph
tools:
- seqwish:
description: |
seqwish implements a lossless conversion from pairwise alignments between
sequences to a variation graph encoding the sequences and their alignments.
homepage: https://github.com/ekg/seqwish
documentation: https://github.com/ekg/seqwish
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 ]
- paf:
type: file
description: PAF file of alignments
pattern: "*.{paf,paf.gz}"
- fasta:
type: file
description: FASTA file used to generate alignments
pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gfa:
type: file
description: Variation graph in GFA1 format
pattern: "*.{gfa}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@heuermh"

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lcl|MT192765.1_cds_QIK50434.1_9 366 6 357 + lcl|MT192765.1_cds_QIK50434.1_9 366 6 357 351 351 60 tp:A:P cm:i:68 s1:i:351 s2:i:0 dv:f:0 rl:i:0
lcl|MT192765.1_cds_QIK50435.1_10 1260 4 1255 + lcl|MT192765.1_cds_QIK50435.1_10 1260 4 1255 1251 1251 60 tp:A:P cm:i:231 s1:i:1251 s2:i:0 dv:f:0 rl:i:0
lcl|MT192765.1_cds_QIK50436.1_11 117 0 116 + lcl|MT192765.1_cds_QIK50436.1_11 117 0 116 116 116 60 tp:A:P cm:i:19 s1:i:116 s2:i:0 dv:f:0 rl:i:0

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@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SEQWISH_INDUCE } from '../../../../software/seqwish/induce/main.nf' addParams( options: [:] )
workflow test_seqwish_induce {
def input = []
input = [ [ id:'GCA_011545545.1_ASM1154554v1_cds_from_genomic' ], // meta map
[ file("${launchDir}/tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf", checkIfExists: true) ],
[ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) ] ]
SEQWISH_INDUCE ( input )
}

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@ -0,0 +1,8 @@
- name: seqwish induce
command: nextflow run ./tests/software/seqwish/induce -entry test_seqwish_induce -c tests/config/nextflow.config
tags:
- seqwish
- seqwish_induce
files:
- path: output/seqwish/GCA_011545545.1_ASM1154554v1_cds_from_genomic.gfa
md5sum: 216a02d3aca322a457c31a62c628548e