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add motus profile.

This commit is contained in:
JIANHONG OU 2022-05-23 08:05:06 -04:00
parent fd71b71929
commit 68d0cc00fa
13 changed files with 256 additions and 5 deletions

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@ -37,6 +37,7 @@ params {
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_motus = true
}
process {

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@ -37,6 +37,7 @@ params {
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_motus = true
}
process {

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@ -37,6 +37,7 @@ params {
run_metaphlan3 = false
run_centrifuge = false
run_diamond = false
run_motus = false
}
process {

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@ -60,6 +60,12 @@
"minimap2/index": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"motus/downloaddb": {
"git_sha": "6393a085c5fcea11963774c041808df169907487"
},
"motus/profile": {
"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
},
"multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
@ -80,4 +86,4 @@
}
}
}
}
}

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@ -0,0 +1,39 @@
process MOTUS_DOWNLOADDB {
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
path motus_downloaddb_script
output:
path "db_mOTU/" , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def software = "${motus_downloaddb_script.simpleName}_copy.py"
"""
## must copy script file to working directory,
## otherwise the reference_db will be download to bin folder
## other than current directory
cp $motus_downloaddb_script ${software}
python ${software} \\
$args \\
-t $task.cpus
## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder.
## mOTUs will check the database version is same version as exec version.
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
END_VERSIONS
"""
}

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@ -0,0 +1,39 @@
name: "motus_downloaddb"
description: Download the mOTUs database
keywords:
- classify
- metagenomics
- fastq
- taxonomic profiling
- database
- download
tools:
- "motus":
description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
homepage: "None"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
licence: "['GPL v3']"
input:
- motus_downloaddb:
type: directory
description: |
The mOTUs downloadDB script source file.
It is the source file installed or
remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
pattern: "downloadDB.py"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: directory
description: The mOTUs database directory
pattern: "db_mOTU"
authors:
- "@jianhong"

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@ -0,0 +1,54 @@
process MOTUS_PROFILE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
tuple val(meta), path(reads)
path db
output:
tuple val(meta), path("*.out"), emit: out
tuple val(meta), path("*.bam"), optional: true, emit: bam
tuple val(meta), path("*.mgc"), optional: true, emit: mgc
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def inputs = reads[0].getExtension() == 'bam' ?
"-i ${reads}" :
reads[0].getExtension() == 'mgc' ? "-m $reads" :
meta.single_end ?
"-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
def refdb = db ? "-db ${db}" : ""
"""
motus profile \\
$args \\
$inputs \\
$refdb \\
-t $task.cpus \\
-n $prefix \\
-o ${prefix}.out
## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder.
## mOTUs will check the database version is same version as exec version.
if [ "$db" == "" ]; then
VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
else
VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,61 @@
name: "motus_profile"
description: Taxonomic meta-omics profiling using universal marker genes
keywords:
- classify
- metagenomics
- fastq
- taxonomic profiling
tools:
- "motus":
description: "Marker gene-based OTU (mOTU) profiling"
homepage: "https://motu-tool.org/"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
licence: "['GPL v3']"
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/fasta files of size 1 and 2 for single-end and paired-end data,
respectively.
Or the intermediate bam file mapped by bwa to the mOTUs database or
the output bam file from motus profile.
Or the intermediate mgc read counts table.
pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
- db:
type: directory
description: |
mOTUs database downloaded by `motus downloadDB`
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- out:
type: file
description: Results with taxonomic classification of each read
pattern: "*.out"
- bam:
type: file
description: Optional intermediate sorted BAM file from BWA
pattern: "*.{bam}"
- mgc:
type: file
description: Optional intermediate mgc read count table file saved with `-M`.
pattern: "*.{mgc}"
authors:
- "@jianhong"

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@ -116,6 +116,11 @@ params {
// diamond
run_diamond = false
diamond_output_format = 'txt'
// mOTUs
run_motus = false
download_motus_db = true
motus_downloaddb_script = 'https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'
}
// Load base.config by default for all pipelines

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@ -409,6 +409,17 @@
"shortread_complexityfilter_fastp_threshold": {
"type": "integer",
"default": 30
},
"run_motus": {
"type": "boolean"
},
"download_motus_db": {
"type": "boolean"
},
"motus_downloaddb_script": {
"type": "string",
"default": "https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py",
"description": "mOTUs database download script path."
}
}
}

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@ -0,0 +1 @@
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar

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@ -2,8 +2,9 @@
// Check input samplesheet and get read channels
//
include { DATABASE_CHECK } from '../../modules/local/database_check'
include { UNTAR } from '../../modules/nf-core/modules/untar/main'
include { DATABASE_CHECK } from '../../modules/local/database_check'
include { UNTAR } from '../../modules/nf-core/modules/untar/main'
include { MOTUS_DOWNLOADDB } from '../../modules/nf-core/modules/motus/downloaddb/main'
workflow DB_CHECK {
take:
@ -20,6 +21,22 @@ workflow DB_CHECK {
.splitCsv ( header:true, sep:',' )
.map { create_db_channels(it) }
// Download database for mOTUs
if( params.run_motus ){
check_motus_db =
parsed_samplesheet.filter{ it[0].tool == "motus" }
.ifEmpty{[]}
if( params.download_motus_db ){
MOTUS_DOWNLOADDB( params.motus_downloaddb_script )
check_motus_db = MOTUS_DOWNLOADDB.out.db
.map{[
[tool: "motus", db_name: "db_mOTU", db_params: ''],
it
]}
}
parsed_samplesheet = parsed_samplesheet.mix(check_motus_db)
}
ch_dbs_for_untar = parsed_samplesheet
.branch {
untar: it[1].toString().endsWith(".tar.gz")

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@ -11,7 +11,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main'
workflow PROFILING {
take:
@ -44,6 +44,7 @@ workflow PROFILING {
centrifuge: it[2]['tool'] == 'centrifuge'
kaiju: it[2]['tool'] == 'kaiju'
diamond: it[2]['tool'] == 'diamond'
motus: it[2]['tool'] == 'motus'
unknown: true
}
@ -186,9 +187,23 @@ workflow PROFILING {
}
if ( params.run_motus ) {
ch_input_for_motus = ch_input_for_profiling.motus
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
}
emit:
profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}