maxibor/mgenottate

Mgenottate: (Meta) GENOme ANNOTTATion

Takes genomes as an input, compute completion/contamination QC metrics with Busco, dereplicates with dREP, and provides a summary table in the end.

mermaid graph LR a[genome fasta]--> b[busco quality assesment] b --> c[dRep genome ANI dereplication] c --> d[MMSeqs2 genome taxonomic_annotation] d --> e[Summary table]

Usage

bash nextflow run maxibor/mgenottate -profile {conda,docker,singularity} --input genome_sheet.csv --busco_db path/to/busco/db --mmseqs2_db_path path/to/mmseqs/db

Input/output options

Define where the pipeline should find input data and save output data.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| input | Path to comma-separated file containing information about the samples and genomes See below for more infos. | string | | True | |
| outdir | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud

An example input file can be found in tests/data/test_samplesheet.csv

It contains 2 columns, the first one being the sample name to which a genome belog, and the second one the path to a genome in fasta file (compressed or not).

Databases

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| busco_db | Path to busco database | string | | True | |
| skip_tax_annotation | Skip taxonomic annotation | bool | False | False | |
| mmseqs2_db_name | Name of mmseqs prebuilt database (required if not db path is provided) | string | | | |
| mmseqs2_db_path | Path to mmseqs database (required if no db name is provided)| string | | | |

See MMSeqs2 wiki for valid MMSeqs DB names.

Tools options

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| busco_mode | Busco mode

Help

One of genome, proteins, or transcriptome

|
string | genome | | |
| busco_lineage | Busco lineage. auto for automatic lineage selection | string | auto | | |
| drep_ani | drep secondary clustering ANI threshold | number | 0.99 | | | | mmseqs2_mem | Amount of memory for MMSeqs2 (in Gb) | string | '14G' | | |
| mmseqs2_search_type | 2 (translated), 3 (nucleotide) or 4 (translated nucleotide backtrace) | integer | null(auto) | | |

Max job request options

Set the top limit for requested resources for any single job.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| max_cpus | Maximum number of CPUs that can be requested for any single job.

Help

Use to set
an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

| integer | 16 | | True |
| max_memory | Maximum amount of memory that can be requested for any single job.

Help

Use to
set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

| string | 128.GB | | True |
| max_time | Maximum amount of time that can be requested for any single job.

Help

Use to set
an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

| string | 240.h | | True |

Generic options

Less common options for the pipeline, typically set in a config file.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| help | Display help text. | boolean | | | True |
| version | Display version and exit. | boolean | | | True |
| publish_dir_mode | Method used to save pipeline results to output directory.

Help

The
Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the
pipeline what method should be used to move these files. See Nextflow
docs for details.

| string | copy | | True |
| monochrome_logs | Do not use coloured log outputs. | boolean | | | True |