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Add documentation for taxpasta module
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sofstam
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3 changed files with 83 additions and 142 deletions
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@ -33,6 +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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- [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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- [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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- [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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- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
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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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- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
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@ -435,6 +436,29 @@ Krona charts will be generated by the pipeline for supported tools (Kraken2, Cen
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The resulting HTML files can be loaded into your web browser for exploration. Each file will have a dropdown to allow you to switch between each sample aligned against the given database of the tool.
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The resulting HTML files can be loaded into your web browser for exploration. Each file will have a dropdown to allow you to switch between each sample aligned against the given database of the tool.
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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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<details markdown="1">
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<summary>Output files</summary>
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- `taxpasta`
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- `<db_name>.<sample_id>*.{tsv,csv,arrow,parquet,biom}`: A list of taxonomic profiler output files. The standard format is the `tsv`. The first column describes the taxonomy ID and the rest of the columns describe the read counts for each sample.
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</details>
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The following report files are used for the taxpasta step:
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- Bracken: `<sample>_<db_name>.tsv`
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- Centrifuge: `<sample_id>.centrifuge.txt`
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- Diamond: `<sample_id>`
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- Kaiju: `<sample_id>_<db_name>.kaijutable.txt`
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- KrakenUniq: `<sample_id>_<db_name>.report.txt`
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- Kraken2: `<sample_id>_<db_name>.report.txt`
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- MALT: `<sample_id>.txt.gz`
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- MetaPhlAn3: `<sample_id>_profile.txt`
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- mOTUs: `<sample_id>.out`
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### MultiQC
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### MultiQC
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<details markdown="1">
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<details markdown="1">
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modules.json
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modules.json
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"adapterremoval": {
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"adapterremoval": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"bbmap/bbduk": {
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"bbmap/bbduk": {
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"branch": "master",
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"branch": "master",
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"modules"
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]
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},
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"bowtie2/align": {
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"bowtie2/align": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"bowtie2/build": {
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"bowtie2/build": {
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"modules"
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"bracken/bracken": {
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"bracken/bracken": {
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"bracken/combinebrackenoutputs": {
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"modules"
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"cat/fastq": {
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"cat/fastq": {
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"branch": "master",
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"modules"
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"centrifuge/centrifuge": {
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"centrifuge/centrifuge": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"modules"
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"centrifuge/kreport": {
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"centrifuge/kreport": {
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"branch": "master",
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"branch": "master",
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"custom/dumpsoftwareversions": {
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"diamond/blastx": {
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"diamond/blastx": {
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"branch": "master",
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"branch": "master",
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"modules"
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"falco": {
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"falco": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/falco/falco.diff"
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"patch": "modules/nf-core/falco/falco.diff"
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},
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},
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"fastp": {
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"fastp": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"modules"
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"fastqc": {
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"fastqc": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"modules"
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]
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},
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},
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"kaiju/kaiju": {
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"kaiju/kaiju": {
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"branch": "master",
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"branch": "master",
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"modules"
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},
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"kaiju/kaiju2krona": {
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"kaiju/kaiju2krona": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"kaiju/kaiju2table": {
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"branch": "master",
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"branch": "master",
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"kraken2/kraken2": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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]
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},
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"krakentools/combinekreports": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"krakentools/kreport2krona": {
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"krakentools/kreport2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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]
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},
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"krakenuniq/preloadedkrakenuniq": {
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"krakenuniq/preloadedkrakenuniq": {
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"branch": "master",
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"branch": "master",
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"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
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]
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},
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"krona/ktimporttaxonomy": {
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"krona/ktimporttaxonomy": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"krona/ktimporttext": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"malt/run": {
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"megan/rma2info": {
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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]
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},
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"metaphlan3/mergemetaphlantables": {
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"metaphlan3/metaphlan3": {
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"minimap2/align": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"minimap2/index": {
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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]
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},
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"motus/merge": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"motus/profile": {
|
"motus/profile": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"multiqc": {
|
"multiqc": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
|
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"porechop/porechop": {
|
"porechop/porechop": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"],
|
||||||
"modules"
|
|
||||||
],
|
|
||||||
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
|
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
|
||||||
},
|
},
|
||||||
"prinseqplusplus": {
|
"prinseqplusplus": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"samtools/bam2fq": {
|
"samtools/bam2fq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"samtools/index": {
|
"samtools/index": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"samtools/stats": {
|
"samtools/stats": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"samtools/view": {
|
"samtools/view": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"taxpasta/merge": {
|
"taxpasta/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4",
|
"git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"untar": {
|
"untar": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -509,6 +509,21 @@
|
||||||
"fa_icon": "fas fa-folder-open",
|
"fa_icon": "fas fa-folder-open",
|
||||||
"description": "Specify path to krona taxonomy directories (required for MALT krona plots)",
|
"description": "Specify path to krona taxonomy directories (required for MALT krona plots)",
|
||||||
"help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package."
|
"help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package."
|
||||||
|
},
|
||||||
|
"taxpasta_add_taxonomy": {
|
||||||
|
"type": "boolean",
|
||||||
|
"description": "The path to a directory containing taxdump files.",
|
||||||
|
"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
|
||||||
|
},
|
||||||
|
"taxpasta_add_samplesheet": {
|
||||||
|
"type": "boolean",
|
||||||
|
"description": "A table with with two columns, one for the sample and one for the taxonomic profile.",
|
||||||
|
"help_text": "If this option is provided, any arguments are ignored."
|
||||||
|
},
|
||||||
|
"taxpasta_standardisation_format": {
|
||||||
|
"type": "string",
|
||||||
|
"default": "tsv",
|
||||||
|
"description": "The desired output format."
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"fa_icon": "fas fa-chart-line"
|
"fa_icon": "fas fa-chart-line"
|
||||||
|
|
@ -767,19 +782,5 @@
|
||||||
{
|
{
|
||||||
"$ref": "#/definitions/reference_genome_options"
|
"$ref": "#/definitions/reference_genome_options"
|
||||||
}
|
}
|
||||||
],
|
]
|
||||||
"properties": {
|
|
||||||
"add_taxonomy": {
|
|
||||||
"type": "string",
|
|
||||||
"default": "false"
|
|
||||||
},
|
|
||||||
"add_samplesheet": {
|
|
||||||
"type": "string",
|
|
||||||
"default": "false"
|
|
||||||
},
|
|
||||||
"standardisation_taxpasta_format": {
|
|
||||||
"type": "string",
|
|
||||||
"default": "tsv"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue