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5 changed files with 6 additions and 7 deletions
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@ -548,7 +548,7 @@ process {
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"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}",
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params.taxpasta_add_taxonomy ? "-p" : "",
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params.taxpasta_add_samplesheet ? "-s" :""
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].join(',').replaceAll(','," ")
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].join(' ').trim()
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}
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publishDir = [
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path: { "${params.outdir}/taxpasta/" },
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@ -33,7 +33,7 @@ params {
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run_kaiju = true
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run_kraken2 = true
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run_bracken = true
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run_malt = false
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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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run_diamond = true
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@ -33,7 +33,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
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- [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics
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- [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
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- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
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- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples for the same classifier/profiler.
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- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples from the same database and classifier/profiler.
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- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
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- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
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@ -438,7 +438,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
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### TAXPASTA
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[TAXPASTA](https://github.com/taxprofiler/taxpasta) is a python package added as a module in nf-core/taxprofiler that can standardise and merge two or more taxonomic profiles across samples into one single table..
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[TAXPASTA](https://github.com/taxprofiler/taxpasta) that standardises and merge two or more taxonomic profiles across samples into one single table. It supports multiple different classifiers simplifying taxonomic classification results between tools and databases.
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<details markdown="1">
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<summary>Output files</summary>
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@ -523,7 +523,8 @@
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"taxpasta_standardisation_format": {
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"type": "string",
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"default": "tsv",
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"description": "The desired output format."
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"description": "The desired output format.",
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"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
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}
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},
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"fa_icon": "fas fa-chart-line"
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@ -90,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
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}
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KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
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ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
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@ -142,7 +141,6 @@ workflow STANDARDISATION_PROFILES {
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ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
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ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
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ch_standardised_tables.dump (tag: 'standardised')
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// mOTUs
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