mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:03:10 +00:00
Merge branch 'dev' into hostremoval-publish-fix
This commit is contained in:
commit
cd3c8f6a89
12 changed files with 159 additions and 17 deletions
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@ -44,6 +44,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
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- [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)
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- [Kaiju](https://kaiju.binf.ku.dk/)
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- [mOTUs](https://motu-tool.org/)
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- [MetaMaps](https://github.com/DiltheyLab/MetaMaps)
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4. Perform optional post-processing with:
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- [bracken](https://ccb.jhu.edu/software/bracken/)
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5. Standardises output tables
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@ -251,7 +251,7 @@ process {
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pattern: '*.txt'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -270,4 +270,13 @@ process {
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]
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}
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withName: KAIJU_KAIJU {
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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}
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@ -22,15 +22,16 @@ params {
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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 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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run_kraken2 = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kraken2 = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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}
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@ -124,6 +124,10 @@ Expected (uncompressed) database files for each tool are as follows:
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- `mpa_v30_CHOCOPhlAn_201901.rev.1.bt2`
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- `mpa_v30_CHOCOPhlAn_201901.rev.2.bt2`
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- `mpa_latest`
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- **Kaiju** output of `kaiju-makedb`. A directory containing:
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- `kaiju_db_*.fmi`
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- `nodes.dmp`
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- `names.dmp`
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## Running the pipeline
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@ -53,6 +53,9 @@
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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},
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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}
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}
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}
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41
modules/nf-core/modules/kaiju/kaiju/main.nf
generated
Normal file
41
modules/nf-core/modules/kaiju/kaiju/main.nf
generated
Normal file
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@ -0,0 +1,41 @@
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process KAIJU_KAIJU {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
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'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
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input:
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tuple val(meta), path(reads)
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path(db)
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output:
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tuple val(meta), path('*.tsv'), emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
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"""
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dbnodes=`find -L ${db} -name "*nodes.dmp"`
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dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
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kaiju \\
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$args \\
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-z $task.cpus \\
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-t \$dbnodes \\
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-f \$dbname \\
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-o ${prefix}.tsv \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
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END_VERSIONS
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"""
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}
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53
modules/nf-core/modules/kaiju/kaiju/meta.yml
generated
Normal file
53
modules/nf-core/modules/kaiju/kaiju/meta.yml
generated
Normal file
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name: kaiju_kaiju
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description: Taxonomic classification of metagenomic sequence data using a protein reference 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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tools:
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- kaiju:
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description: Fast and sensitive taxonomic classification for metagenomics
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homepage: https://kaiju.binf.ku.dk/
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documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
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tool_dev_url: https://github.com/bioinformatics-centre/kaiju
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doi: "10.1038/ncomms11257"
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licence: ["GNU 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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pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
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- db:
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type: files
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description: |
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List containing the database and nodes files for Kaiju
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e.g. [ 'database.fmi', 'nodes.dmp' ]
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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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- results:
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type: file
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description: Results with taxonomic classification of each read
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pattern: "*.tsv"
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authors:
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- "@talnor"
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- "@sofstam"
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- "@jfy133"
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@ -104,6 +104,9 @@ params {
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// metaphlan3
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run_metaphlan3 = false
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// kaiju
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run_kaiju = false
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}
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// Load base.config by default for all pipelines
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@ -379,6 +379,9 @@
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"save_hostremoval_unmapped": {
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"type": "boolean"
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},
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"run_kaiju": {
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"type": "boolean"
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},
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"malt_generatemegansummary": {
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"type": "boolean"
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}
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@ -45,6 +45,7 @@ def create_fastq_channel(LinkedHashMap row) {
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = row.single_end.toBoolean()
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meta.is_fasta = false
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// add path(s) of the fastq file(s) to the meta map
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def fastq_meta = []
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = true
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meta.is_fasta = true
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def array = []
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if (!file(row.fasta).exists()) {
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@ -7,6 +7,7 @@ include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/mega
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
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include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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workflow PROFILING {
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take:
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kraken2: it[2]['tool'] == 'kraken2'
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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centrifuge: it[2]['tool'] == 'centrifuge'
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kaiju: it[2]['tool'] == 'kaiju'
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unknown: true
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}
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@ -77,13 +79,28 @@ workflow PROFILING {
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}
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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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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.filter{
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge 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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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.filter{
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 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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ch_input_for_kaiju = ch_input_for_profiling.kaiju
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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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@ -135,6 +152,10 @@ workflow PROFILING {
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ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
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}
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if ( params.run_kaiju ) {
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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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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@ -19,11 +19,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
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if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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@ -175,10 +175,11 @@ workflow TAXPROFILER {
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meta, reads ->
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[ meta, [ reads ].flatten() ]
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}
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.mix( INPUT_CHECK.out.fasta )
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} else {
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ch_reads_runmerged = ch_shortreads_hostremoved
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.mix( ch_longreads_preprocessed )
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.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
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}
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/*
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