New module to use hmmalign from HMMER to align sequences (#470)

* Ignore vim tmp files

* Added hmmalign module, not yet tests

* Test output

* Replaced functions.nf for hmmalign with upstream

* Update software/hmmer/hmmalign/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/hmmer/hmmalign/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/hmmer/hmmalign/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/hmmer/hmmalign/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/hmmer/hmmalign/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/hmmer/hmmalign/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/hmmer/hmmalign/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Daniel Lundin 2021-04-28 12:21:24 +02:00 committed by GitHub
parent d63ff4ba1b
commit d7a3286a9a
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7 changed files with 188 additions and 0 deletions

2
.gitignore vendored
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@ -5,3 +5,5 @@ test_output/
output/
.DS_Store
*.code-workspace
.screenrc
.*.sw?

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@ -0,0 +1,70 @@
/*
* -----------------------------------------------------
* 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"
}
}
}

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@ -0,0 +1,42 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process HMMER_HMMALIGN {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1"
} else {
container "quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1"
}
input:
tuple val(meta), path(fasta)
path hmm
output:
tuple val(meta), path("*.sthlm.gz"), emit: sthlm
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def fastacmd = fasta.getExtension() == 'gz' ? "gunzip -c $fasta" : "cat $fasta"
"""
$fastacmd | \\
hmmalign \\
$options.args \\
$hmm \\
- | gzip -c > ${meta.id}.sthlm.gz
echo \$(hmmalign -h | grep -o '^# HMMER [0-9.]*') | sed 's/^# HMMER *//' > ${software}.version.txt
"""
}

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@ -0,0 +1,45 @@
name: hmmer_hmmalign
description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
keywords:
- alignment
tools:
- hmmer:
description: Biosequence analysis using profile hidden Markov models
homepage: http://hmmer.org/
documentation: http://hmmer.org/documentation.html
tool_dev_url: None
doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
licence: ['BSD']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- fasta:
type: file
description: Amino acid or nucleotide fasta file, gzipped or not
pattern: "*.{fna,fna.gz,faa,faa.gz,fasta,fasta.gz,fa,fa.gz}"
- hmm:
type: file
description: HMM file
pattern: "*.hmm"
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}"
- sthlm:
type: file
description: Multiple alignment in gzipped Stockholm format
pattern: "*.sthlm.gz"
authors:
- "@erikrikarddaniel"

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@ -297,6 +297,10 @@ hisat2/extractsplicesites:
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/extractsplicesites/**
hmmer/hmmalign:
- software/hmmer/hmmalign/**
- tests/software/hmmer/hmmalign/**
homer/annotatepeaks:
- software/homer/annotatepeaks/**
- tests/software/homer/annotatepeaks/**

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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HMMER_HMMALIGN } from '../../../../software/hmmer/hmmalign/main.nf' addParams( options: [:] )
workflow test_hmmer_hmmalign {
input = [
[ id:'test' ], // meta map
file('https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/modules/data/delete_me/e_coli_k12_16s.fna') // Change to params.test_data syntax after the data is included in tests/config/test_data.config
]
hmm = file('https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/modules/data/delete_me/bac.16S_rRNA.hmm')
HMMER_HMMALIGN ( input, hmm )
}

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- name: hmmer hmmalign test_hmmer_hmmalign
command: nextflow run tests/software/hmmer/hmmalign -entry test_hmmer_hmmalign -c tests/config/nextflow.config
tags:
- hmmer
- hmmer/hmmalign
files:
- path: output/hmmer/test.sthlm.gz
md5sum: ddaa8b96291edf4e1a929a224329161b