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Add spades module (#277)

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* Add spades module

* Reorder gatk4 modules alphabetically

* Update software/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Jose Espinosa-Carrasco 2021-03-18 14:48:38 +01:00 committed by GitHub
parent 313241749c
commit 72e81d6e90
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6 changed files with 325 additions and 7 deletions
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60
software/spades/functions.nf Normal file
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@ -0,0 +1,60 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

69
software/spades/main.nf Normal file
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SPADES {
tag "$meta.id"
label 'process_high'
publishDir "${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::spades=3.15.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
} else {
container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
}
input:
tuple val(meta), path(reads)
path hmm
val coronaspades
output:
tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
tuple val(meta), path('*.contigs.fa') , optional:true, emit: contigs
tuple val(meta), path('*.transcripts.fa') , optional:true, emit: transcripts
tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters
tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa
tuple val(meta), path('*.log') , emit: log
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
def command = coronaspades ? "coronaspades.py" : "spades.py"
"""
$command \\
$options.args \\
--threads $task.cpus \\
$custom_hmms \\
$input_reads \\
-o ./
mv spades.log ${prefix}.spades.log
if [ -f scaffolds.fasta ]; then
mv scaffolds.fasta ${prefix}.scaffolds.fa
fi
if [ -f contigs.fasta ]; then
mv contigs.fasta ${prefix}.contigs.fa
fi
if [ -f transcripts.fasta ]; then
mv transcripts.fasta ${prefix}.transcripts.fa
fi
if [ -f assembly_graph_with_scaffolds.gfa ]; then
mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa
fi
if [ -f gene_clusters.fasta ]; then
mv gene_clusters.fasta ${prefix}.gene_clusters.fa
fi
echo \$(spades.py --version 2>&1) | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//' > ${software}.version.txt
"""
}

74
software/spades/meta.yml Normal file
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name: spades
description: Assembles a small genome (bacterial, fungal, viral)
keywords:
- genome
- assembly
- genome assembler
- small genome
- de novo assembler
tools:
- spades:
description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
homepage: http://cab.spbu.ru/files/release3.15.0/manual.html
documentation: http://cab.spbu.ru/files/release3.15.0/manual.html
tool_dev_url: https://github.com/ablab/spades
doi: 10.1089/cmb.2012.0021
licence: ['GPL v2']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- hmm:
type: file
description:
File or directory with amino acid HMMs for Spades HMM-guided mode.
- coronaspades:
type: boolean
description: |
Run coronaspades instead of default spades mode. coronaSPAdes is a special
mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- scaffolds:
type: file
description: |
Fasta file containing scaffolds
- contigs:
type: file
description: |
Fasta file containing contigs
- transcripts:
type: file
description: |
Fasta file containing transcripts
- gene_clusters:
type: file
description: |
Fasta file containing gene_clusters
- gfa:
type: file
description: |
gfa file containing assembly
- log:
type: file
description: |
Spades log file
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@JoseEspinosa"
- "@drpatelh"

19
tests/config/pytest_software.yml
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@ -144,6 +144,10 @@ gatk4_createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
gatk4_mergevcfs:
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
@ -160,6 +164,10 @@ gatk4_splitncigarreads:
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
gffread:
- software/gffread/**
- tests/software/gffread/**
@ -289,6 +297,10 @@ seqwish_induce:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
spades:
- software/spades/**
- tests/software/spades/**
star_align:
- software/star/align/**
- tests/software/star/align/**
@ -325,10 +337,3 @@ untar:
- software/untar/**
- tests/software/untar/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**

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tests/software/spades/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
workflow test_spades_single_end {
def input = []
def hmm = []
def coronaspades = false
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] ]
SPADES ( input, hmm, coronaspades )
}
workflow test_spades_paired_end {
def input = []
def hmm = []
def coronaspades = false
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ]
SPADES ( input, hmm, coronaspades )
}
workflow test_coronospades_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
def hmm = []
def coronaspades = true
SPADES ( input, hmm, coronaspades )
}
workflow test_coronospades_paired_end {
def input = []
def hmm = []
def coronaspades = true
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
SPADES ( input, hmm, coronaspades )
}

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tests/software/spades/test.yml Normal file
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- name: spades single end
command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config
tags:
- spades
- spades_single_end
files:
- path: output/spades/test.assembly.gfa
md5sum: f15ad4a198324de37c6010dafb3fe781
- path: output/spades/test.contigs.fa
md5sum: bc21771042b465c26dfc85beedc33d58
- path: output/spades/test.scaffolds.fa
md5sum: bc21771042b465c26dfc85beedc33d58
- path: output/spades/test.spades.log
- path: output/spades/warnings.log
- name: spades paired end
command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
tags:
- spades
- spades_paired_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 5da5b04c6fce549c77a209034a9c1e72
- path: output/spades/test.contigs.fa
md5sum: 403b612d52edf390f662ab601873f09f
- path: output/spades/test.scaffolds.fa
md5sum: 49a9cbb29cee4d088e05e62eb4bc77c4
- path: output/spades/test.spades.log
- path: output/spades/warnings.log
- name: coronaspades single end
command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
tags:
- spades
- coronaspades_single_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 46531ec9b845c1a1cb469627688fecb7
- path: output/spades/test.contigs.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.scaffolds.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.spades.log
- name: coronaspades paired end
command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
tags:
- spades
- coronaspades_paired_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 46531ec9b845c1a1cb469627688fecb7
- path: output/spades/test.contigs.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.scaffolds.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.spades.log