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.

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]

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Usage

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
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](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.	string	copy		True
monochrome_logs	Do not use coloured log outputs.	boolean			True