mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 05:59:56 +00:00
Add documentation for taxpasta module
This commit is contained in:
sofstam
parent
25d44c955e
commit
dad64a688d
3 changed files with 83 additions and 142 deletions
|
|
@ -33,6 +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.
|
||||||
- [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
|
||||||
|
|
||||||
|
|
@ -435,6 +436,29 @@ Krona charts will be generated by the pipeline for supported tools (Kraken2, Cen
|
||||||
|
|
||||||
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.
|
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.
|
||||||
|
|
||||||
|
### 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..
|
||||||
|
|
||||||
|
<details markdown="1">
|
||||||
|
<summary>Output files</summary>
|
||||||
|
|
||||||
|
- `taxpasta`
|
||||||
|
- `<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.
|
||||||
|
</details>
|
||||||
|
|
||||||
|
The following report files are used for the taxpasta step:
|
||||||
|
|
||||||
|
- Bracken: `<sample>_<db_name>.tsv`
|
||||||
|
- Centrifuge: `<sample_id>.centrifuge.txt`
|
||||||
|
- Diamond: `<sample_id>`
|
||||||
|
- Kaiju: `<sample_id>_<db_name>.kaijutable.txt`
|
||||||
|
- KrakenUniq: `<sample_id>_<db_name>.report.txt`
|
||||||
|
- Kraken2: `<sample_id>_<db_name>.report.txt`
|
||||||
|
- MALT: `<sample_id>.txt.gz`
|
||||||
|
- MetaPhlAn3: `<sample_id>_profile.txt`
|
||||||
|
- mOTUs: `<sample_id>.out`
|
||||||
|
|
||||||
### MultiQC
|
### MultiQC
|
||||||
|
|
||||||
<details markdown="1">
|
<details markdown="1">
|
||||||
|
|
|
||||||
170
modules.json
170
modules.json
|
|
@ -8,301 +8,217 @@
|
||||||
"adapterremoval": {
|
"adapterremoval": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"bbmap/bbduk": {
|
"bbmap/bbduk": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"bowtie2/align": {
|
"bowtie2/align": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"bowtie2/build": {
|
"bowtie2/build": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"bracken/bracken": {
|
"bracken/bracken": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"bracken/combinebrackenoutputs": {
|
"bracken/combinebrackenoutputs": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"cat/fastq": {
|
"cat/fastq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"centrifuge/centrifuge": {
|
"centrifuge/centrifuge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"centrifuge/kreport": {
|
"centrifuge/kreport": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"custom/dumpsoftwareversions": {
|
"custom/dumpsoftwareversions": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"diamond/blastx": {
|
"diamond/blastx": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"falco": {
|
"falco": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"],
|
||||||
"modules"
|
|
||||||
],
|
|
||||||
"patch": "modules/nf-core/falco/falco.diff"
|
"patch": "modules/nf-core/falco/falco.diff"
|
||||||
},
|
},
|
||||||
"fastp": {
|
"fastp": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"fastqc": {
|
"fastqc": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"filtlong": {
|
"filtlong": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"gunzip": {
|
"gunzip": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"kaiju/kaiju": {
|
"kaiju/kaiju": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"kaiju/kaiju2krona": {
|
"kaiju/kaiju2krona": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"kaiju/kaiju2table": {
|
"kaiju/kaiju2table": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"kraken2/kraken2": {
|
"kraken2/kraken2": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"krakentools/combinekreports": {
|
"krakentools/combinekreports": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"krakentools/kreport2krona": {
|
"krakentools/kreport2krona": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"krakenuniq/preloadedkrakenuniq": {
|
"krakenuniq/preloadedkrakenuniq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
|
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"krona/ktimporttaxonomy": {
|
"krona/ktimporttaxonomy": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"krona/ktimporttext": {
|
"krona/ktimporttext": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"malt/run": {
|
"malt/run": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"megan/rma2info": {
|
"megan/rma2info": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"metaphlan3/mergemetaphlantables": {
|
"metaphlan3/mergemetaphlantables": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"metaphlan3/metaphlan3": {
|
"metaphlan3/metaphlan3": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"minimap2/align": {
|
"minimap2/align": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"minimap2/index": {
|
"minimap2/index": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": [
|
"installed_by": ["modules"]
|
||||||
"modules"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"motus/merge": {
|
"motus/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"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