mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:53:10 +00:00
commit
1eba859bf8
14 changed files with 258 additions and 3 deletions
51
.github/workflows/ci.yml
vendored
51
.github/workflows/ci.yml
vendored
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@ -71,3 +71,54 @@ jobs:
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
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motus:
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name: Test mOTUs with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions
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include:
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# Test pipeline minimum Nextflow version
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- NXF_VER: "21.10.3"
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NXF_EDGE: ""
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# Test latest edge release of Nextflow
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- NXF_VER: ""
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NXF_EDGE: "1"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Show current locale
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run: locale
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- name: Set UTF-8 enabled locale
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run: |
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sudo locale-gen en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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- name: Prepare the database
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run: |
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wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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python downloadDB.py > download_db_log.txt
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echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
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echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
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@ -365,6 +365,13 @@ process {
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]
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}
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withName: MOTUS_PROFILE {
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publishDir = [
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path: { "${params.outdir}/motus/${meta.db_name}" },
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mode: params.publish_dir_mode
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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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 = false
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run_krona = true
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malt_save_reads = true
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kraken2_save_reads = true
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41
conf/test_motus.config
Normal file
41
conf/test_motus.config
Normal file
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@ -0,0 +1,41 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'mOTUs Test profile'
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config_profile_description = 'Minimal test to check mOTUs function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'database_motus.csv'
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perform_shortread_clipmerge = false
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perform_longread_clip = false
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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perform_runmerging = false
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = false
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run_kraken2 = false
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run_malt = false
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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 = true
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}
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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 = false
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run_krona = true
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}
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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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@ -79,6 +79,7 @@ kraken2,db1,,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
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metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
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motus,db_mOTU,,/<path>/<to>/motus/motus_database/
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```
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Column specifications are as follows:
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@ -133,6 +134,13 @@ Expected (uncompressed) database files for each tool are as follows:
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- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
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to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
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- `<database_name>.dmnd`
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- **mOTUs** is composed of code and database together. The mOTUs tools
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[`downloadDB`](https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py)
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is used to prepare the mOTUs database and create a file with the version information.
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The database download step can be time consuming and the database will be consisting
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with same release version of the mOTUs tools. The database for same version tools
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can be thus reused for multiple runs. Users can download the database once using the script above and
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specify the path the database to the TSV table provided to `--databases`.
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## Running the pipeline
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@ -72,6 +72,9 @@
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"minimap2/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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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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54
modules/nf-core/modules/motus/profile/main.nf
generated
Normal file
54
modules/nf-core/modules/motus/profile/main.nf
generated
Normal file
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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
generated
Normal file
61
modules/nf-core/modules/motus/profile/meta.yml
generated
Normal file
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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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@ -126,6 +126,9 @@ params {
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diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
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diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
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// mOTUs
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run_motus = false
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// krona
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run_krona = false
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}
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@ -200,6 +203,7 @@ profiles {
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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}
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// Load igenomes.config if required
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@ -421,6 +421,9 @@
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"type": "integer",
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"default": 500000000
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},
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"run_motus": {
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"type": "boolean"
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},
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"malt_save_reads": {
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"type": "boolean"
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},
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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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@ -45,6 +45,7 @@ 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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@ -210,6 +211,25 @@ 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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.filter{
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] mOTUs currently does not accept FASTA files as input. Skipping mOTUs for sample ${it[0].id}."
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!it[0].is_fasta
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}
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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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classifications = ch_raw_classifications
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profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
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|
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