mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
add motus profile.
This commit is contained in:
parent
fd71b71929
commit
68d0cc00fa
13 changed files with 256 additions and 5 deletions
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@ -37,6 +37,7 @@ params {
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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run_motus = true
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}
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process {
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@ -37,6 +37,7 @@ params {
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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run_motus = true
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}
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process {
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@ -37,6 +37,7 @@ params {
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run_metaphlan3 = false
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run_centrifuge = false
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run_diamond = false
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run_motus = false
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}
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process {
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@ -60,6 +60,12 @@
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"minimap2/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"motus/downloaddb": {
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"git_sha": "6393a085c5fcea11963774c041808df169907487"
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},
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"motus/profile": {
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"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
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},
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"multiqc": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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@ -80,4 +86,4 @@
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}
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}
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}
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}
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}
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39
modules/nf-core/modules/motus/downloaddb/main.nf
generated
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39
modules/nf-core/modules/motus/downloaddb/main.nf
generated
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@ -0,0 +1,39 @@
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process MOTUS_DOWNLOADDB {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
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'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
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input:
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path motus_downloaddb_script
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output:
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path "db_mOTU/" , emit: db
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def software = "${motus_downloaddb_script.simpleName}_copy.py"
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"""
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## must copy script file to working directory,
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## otherwise the reference_db will be download to bin folder
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## other than current directory
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cp $motus_downloaddb_script ${software}
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python ${software} \\
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$args \\
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-t $task.cpus
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## mOTUs version number is not available from command line.
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## mOTUs save the version number in index database folder.
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## mOTUs will check the database version is same version as exec version.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
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END_VERSIONS
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"""
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}
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39
modules/nf-core/modules/motus/downloaddb/meta.yml
generated
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39
modules/nf-core/modules/motus/downloaddb/meta.yml
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@ -0,0 +1,39 @@
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name: "motus_downloaddb"
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description: Download the mOTUs database
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keywords:
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- classify
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- metagenomics
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- fastq
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- taxonomic profiling
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- database
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- download
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tools:
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- "motus":
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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."
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homepage: "None"
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documentation: "https://github.com/motu-tool/mOTUs/wiki"
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tool_dev_url: "https://github.com/motu-tool/mOTUs"
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doi: "10.1038/s41467-019-08844-4"
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licence: "['GPL v3']"
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input:
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- motus_downloaddb:
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type: directory
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description: |
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The mOTUs downloadDB script source file.
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It is the source file installed or
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remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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pattern: "downloadDB.py"
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output:
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- db:
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type: directory
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description: The mOTUs database directory
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pattern: "db_mOTU"
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authors:
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- "@jianhong"
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54
modules/nf-core/modules/motus/profile/main.nf
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54
modules/nf-core/modules/motus/profile/main.nf
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@ -0,0 +1,54 @@
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process MOTUS_PROFILE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
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'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(reads)
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path db
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output:
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tuple val(meta), path("*.out"), emit: out
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tuple val(meta), path("*.bam"), optional: true, emit: bam
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tuple val(meta), path("*.mgc"), optional: true, emit: mgc
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def inputs = reads[0].getExtension() == 'bam' ?
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"-i ${reads}" :
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reads[0].getExtension() == 'mgc' ? "-m $reads" :
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meta.single_end ?
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"-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
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def refdb = db ? "-db ${db}" : ""
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"""
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motus profile \\
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$args \\
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$inputs \\
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$refdb \\
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-t $task.cpus \\
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-n $prefix \\
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-o ${prefix}.out
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## mOTUs version number is not available from command line.
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## mOTUs save the version number in index database folder.
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## mOTUs will check the database version is same version as exec version.
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if [ "$db" == "" ]; then
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VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
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else
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VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mOTUs: \$VERSION
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END_VERSIONS
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"""
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}
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61
modules/nf-core/modules/motus/profile/meta.yml
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61
modules/nf-core/modules/motus/profile/meta.yml
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name: "motus_profile"
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description: Taxonomic meta-omics profiling using universal marker genes
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keywords:
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- classify
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- metagenomics
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- fastq
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- taxonomic profiling
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tools:
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- "motus":
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description: "Marker gene-based OTU (mOTU) profiling"
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homepage: "https://motu-tool.org/"
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documentation: "https://github.com/motu-tool/mOTUs/wiki"
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tool_dev_url: "https://github.com/motu-tool/mOTUs"
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doi: "10.1038/s41467-019-08844-4"
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licence: "['GPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
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respectively.
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Or the intermediate bam file mapped by bwa to the mOTUs database or
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the output bam file from motus profile.
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Or the intermediate mgc read counts table.
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pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
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- db:
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type: directory
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description: |
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mOTUs database downloaded by `motus downloadDB`
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- out:
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type: file
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description: Results with taxonomic classification of each read
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pattern: "*.out"
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- bam:
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type: file
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description: Optional intermediate sorted BAM file from BWA
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pattern: "*.{bam}"
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- mgc:
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type: file
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description: Optional intermediate mgc read count table file saved with `-M`.
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pattern: "*.{mgc}"
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authors:
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- "@jianhong"
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@ -116,6 +116,11 @@ params {
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// diamond
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run_diamond = false
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diamond_output_format = 'txt'
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// mOTUs
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run_motus = false
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download_motus_db = true
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motus_downloaddb_script = 'https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'
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}
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// Load base.config by default for all pipelines
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@ -409,6 +409,17 @@
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"shortread_complexityfilter_fastp_threshold": {
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"type": "integer",
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"default": 30
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},
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"run_motus": {
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"type": "boolean"
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},
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"download_motus_db": {
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"type": "boolean"
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},
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"motus_downloaddb_script": {
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"type": "string",
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"default": "https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py",
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"description": "mOTUs database download script path."
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}
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}
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}
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@ -0,0 +1 @@
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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 @@
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// Check input samplesheet and get read channels
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//
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { UNTAR } from '../../modules/nf-core/modules/untar/main'
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { UNTAR } from '../../modules/nf-core/modules/untar/main'
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include { MOTUS_DOWNLOADDB } from '../../modules/nf-core/modules/motus/downloaddb/main'
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workflow DB_CHECK {
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take:
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@ -20,6 +21,22 @@ workflow DB_CHECK {
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.splitCsv ( header:true, sep:',' )
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.map { create_db_channels(it) }
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// Download database for mOTUs
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if( params.run_motus ){
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check_motus_db =
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parsed_samplesheet.filter{ it[0].tool == "motus" }
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.ifEmpty{[]}
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if( params.download_motus_db ){
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MOTUS_DOWNLOADDB( params.motus_downloaddb_script )
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check_motus_db = MOTUS_DOWNLOADDB.out.db
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.map{[
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[tool: "motus", db_name: "db_mOTU", db_params: ''],
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it
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]}
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}
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parsed_samplesheet = parsed_samplesheet.mix(check_motus_db)
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}
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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untar: it[1].toString().endsWith(".tar.gz")
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@ -11,7 +11,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
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include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main'
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workflow PROFILING {
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take:
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@ -44,6 +44,7 @@ workflow PROFILING {
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centrifuge: it[2]['tool'] == 'centrifuge'
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kaiju: it[2]['tool'] == 'kaiju'
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diamond: it[2]['tool'] == 'diamond'
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motus: it[2]['tool'] == 'motus'
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unknown: true
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}
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@ -186,9 +187,23 @@ workflow PROFILING {
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}
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if ( params.run_motus ) {
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ch_input_for_motus = ch_input_for_profiling.motus
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
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ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
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}
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emit:
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profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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