Add snpeff (#546)

* feat: add snpeff

* fix: linting

* fix: tests

* fix: add csv output

* fix: add params information

* fix: improve script

* Update software/snpeff/environment.yml

* Update software/snpeff/environment.yml

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

* Apply suggestions from code review

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

* Apply suggestions from code review

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

* Apply suggestions from code review

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

* Apply suggestions from code review

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Maxime U. Garcia 2021-07-06 14:40:55 +02:00 committed by GitHub
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commit e0d820f9f4
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FROM nfcore/base:1.14
LABEL \
author="Maxime Garcia" \
description="snpEff image for nf-core pipelines" \
maintainer="maxime.garcia@scilifelab.se"
# Install the conda environment
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SNPEFF_CACHE_VERSION=99
# Download Genome
RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-snpeff-5.0 > nf-core-snpeff-5.0.yml

24
software/snpeff/build.sh Executable file
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#!/usr/bin/env bash
set -euo pipefail
# Build and push all containers
build_push() {
GENOME=$1
SNPEFF_CACHE_VERSION=$2
SNPEFF_TAG=$3
docker build \
-t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \
software/snpeff/. \
--build-arg GENOME=${GENOME} \
--build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME}
}
build_push "GRCh37" "75" "5.0"
build_push "GRCh38" "99" "5.0"
build_push "GRCm38" "99" "5.0"
build_push "CanFam3.1" "99" "5.0"
build_push "WBcel235" "99" "5.0"

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# You can use this file to create a conda environment for this module:
# conda env create -f environment.yml
name: nf-core-snpeff-5.0
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::snpeff=5.0

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//
// Utility functions used in nf-core DSL2 module files
//
//
// Extract name of software tool from process name using $task.process
//
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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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software/snpeff/main.nf Normal file
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
params.use_cache = false
params.snpeff_tag = ""
process SNPEFF {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
if (params.use_cache) {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1"
} else {
container "quay.io/biocontainers/snpeff:5.0--hdfd78af_1"
}
} else {
container "nfcore/snpeff:${params.snpeff_tag}"
}
input:
tuple val(meta), path(vcf)
val db
path cache
output:
tuple val(meta), path("*.ann.vcf"), emit: vcf
path "*.csv" , emit: report
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def avail_mem = 6
if (!task.memory) {
log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
cache = params.use_cache ? "-dataDir \${PWD}/${snpeff_cache}" : ""
"""
snpEff -Xmx${avail_mem}g \\
$db \\
$options.args \\
-csvStats ${prefix}.csv \\
$cache \\
$vcf \\
> ${prefix}.ann.vcf
echo \$(snpEff -version 2>&1) > ${software}.version.txt
"""
}

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software/snpeff/meta.yml Normal file
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name: snpEff
description: Genetic variant annotation and functional effect prediction toolbox
keywords:
- annotation
tools:
- snpeff:
description: |
SnpEff is a variant annotation and effect prediction tool.
It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
homepage: https://pcingola.github.io/SnpEff/
documentation: https://pcingola.github.io/SnpEff/se_introduction/
params:
- use_cache:
type: boolean
description: |
boolean to enable the usage of containers with cache
Enable the usage of containers with cache
Does not work with conda
- snpeff_tag:
type: value
description: |
Specify the tag for the container
https://hub.docker.com/r/nfcore/snpeff/tags
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
vcf to annotate
- db:
type: value
description: |
which db to annotate with
- cache:
type: file
description: |
path to snpEff cache (optional)
output:
- vcf:
type: file
description: |
annotated vcf
pattern: "*.ann.vcf"
- report:
type: file
description: snpEff report file
pattern: "*.html"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@maxulysse"

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@ -719,6 +719,10 @@ shovill:
- software/shovill/**
- tests/software/shovill/**
snpeff:
- software/snpeff/**
- tests/software/snpeff/**
snpsites:
- software/snpsites/**
- tests/software/snpsites/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNPEFF } from '../../../software/snpeff/main.nf' addParams( snpeff_tag: '5.0.WBcel235', use_cache: false )
workflow test_snpeff {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
]
SNPEFF ( input, "WBcel235.99", [] )
}

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- name: snpeff test_snpeff
command: nextflow run tests/software/snpeff -entry test_snpeff -c tests/config/nextflow.config
tags:
- snpeff
files:
- path: output/snpeff/test.ann.vcf
md5sum: 42db84cb186e33c6992f9306627201ac
- path: output/snpeff/test.csv