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sofstam 2023-02-17 09:16:58 +01:00
parent c9b521234b
commit 27b7171b96
5 changed files with 6 additions and 7 deletions
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2
conf/modules.config
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@ -548,7 +548,7 @@ process {
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}", "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}",
params.taxpasta_add_taxonomy ? "-p" : "", params.taxpasta_add_taxonomy ? "-p" : "",
params.taxpasta_add_samplesheet ? "-s" :"" params.taxpasta_add_samplesheet ? "-s" :""
].join(',').replaceAll(','," ") ].join(' ').trim()
} }
publishDir = [ publishDir = [
path: { "${params.outdir}/taxpasta/" }, path: { "${params.outdir}/taxpasta/" },

2
conf/test.config
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@ -33,7 +33,7 @@ params {
run_kaiju = true run_kaiju = true
run_kraken2 = true run_kraken2 = true
run_bracken = true run_bracken = true
run_malt = false run_malt = true
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true

4
docs/output.md
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@ -33,7 +33,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics - [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics
- [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier - [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling. - [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples for the same classifier/profiler. - [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples from the same database and classifier/profiler.
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@ -438,7 +438,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
### TAXPASTA ### TAXPASTA
[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.. [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.
<details markdown="1"> <details markdown="1">
<summary>Output files</summary> <summary>Output files</summary>

3
nextflow_schema.json
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@ -523,7 +523,8 @@
"taxpasta_standardisation_format": { "taxpasta_standardisation_format": {
"type": "string", "type": "string",
"default": "tsv", "default": "tsv",
"description": "The desired output format." "description": "The desired output format.",
"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
} }
}, },
"fa_icon": "fas fa-chart-line" "fa_icon": "fas fa-chart-line"

2
subworkflows/local/standardisation_profiles.nf
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@ -90,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
} }
KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge ) KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt ) ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
@ -142,7 +141,6 @@ workflow STANDARDISATION_PROFILES {
ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt ) ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions ) ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
ch_standardised_tables.dump (tag: 'standardised')
// mOTUs // mOTUs