adding fasttree module (#412)

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* remove TODO

* update test data naming

* further test data naming updates

* remove options in favour of $options.args

* ensure non standard exit codes don't cause an issue

* update md5sum
This commit is contained in:
Anthony Underwood 2021-04-08 18:15:23 +01:00 committed by GitHub
parent a3684d9594
commit be390a25e5
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
9 changed files with 172 additions and 2 deletions

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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"
}
}
}

38
software/fasttree/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 FASTTREE {
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:'') }
conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4"
} else {
container "quay.io/biocontainers/fasttree:2.1.10--h516909a_4"
}
input:
path alignment
output:
path "*.tre", emit: phylogeny
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
fasttree \\
$options.args \\
-log fasttree_phylogeny.tre.log \\
-nt $alignment \\
> fasttree_phylogeny.tre
echo \$(fasttree -help 2>&1) | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/' > ${software}.version.txt
"""
}

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name: fasttree
description: Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments.
keywords:
- phylogeny
- newick
tools:
- fasttree:
description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
homepage: http://www.microbesonline.org/fasttree/
documentation: http://www.microbesonline.org/fasttree/#Usage
tool_dev_url: None
doi: ""
licence: ['GPL v2']
input:
- alignment:
type: file
description: A FASTA format multiple sequence alignment file
pattern: "*.{fasta,fas,fa,mfa}"
output:
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- phylogeny:
type: file
description: A phylogeny in Newick format
pattern: "*.{tre}"
authors:
- "@aunderwo"

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@ -178,6 +178,10 @@ fastqc:
- software/fastqc/**
- tests/software/fastqc/**
fasttree:
- software/fasttree/**
- tests/software/fasttree/**
fgbio_callmolecularconsensusreads:
- software/fgbio/callmolecularconsensusreads/**
- tests/software/fgbio/callmolecularconsensusreads/**

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@ -25,8 +25,9 @@ params {
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
test_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
}
'illumina' {
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

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>sample1
CCCCAGCCTTNTTGGTTCCTANNTCTACCCCTCTGTGGNCCGAGATGGGTCTAT
>sample2
TCTTGTATCCCCCGGCCTTCGGCCTCTAGATTCGCCGCNCTTGCTAAACCTGTG
>sample3
CCCCGGCCTCTCCGGCCCCTACTTCCACGCCTTTGCGGTTCGAGATGGGTCGTT
>sample4
TTCCGGCCCCTCCTTCCCCTAGCCCCACGCCCCTGCTCCCCGAGATAACCCGTG

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTTREE } from '../../../software/fasttree/main.nf' addParams( options: [:] )
workflow test_fasttree {
input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
FASTTREE ( input )
}

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- name: fasttree
command: nextflow run ./tests/software/fasttree -entry test_fasttree -c tests/config/nextflow.config
tags:
- fasttree
files:
- path: output/fasttree/fasttree_phylogeny.tre
md5sum: 63a886117535847c1e66fa4487f3b7d2