busco/busco_run

Genome assembly

quality control

Description

Assessment of genome assembly and annotation completeness with single copy orthologs

Inputs

Name	Type & Properties	Description
--input -i	file required	Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.
--mode -m	string required	Specify which BUSCO analysis mode to run. There are three valid modes: - geno or genome, for genome assemblies (DNA) - tran or transcriptome, for transcriptome assemblies (DNA) - prot or proteins, for annotated gene sets (protein)
--lineage_dataset -l	string	Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component. When unsure, the "--auto_lineage" flag can be set to automatically find the optimal lineage path. BUSCO will automatically download the requested dataset if it is not already present in the download folder. You can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset. Datasets can be downloaded using the busco/busco_download_dataset component.

Name

Type & Properties

--input

-i

file

required

--mode

-m

string

required

--lineage_dataset

-l

string

Outputs

Name	Type & Properties	Description
--short_summary_json	file output	Output file for short summary in JSON format.
--short_summary_txt	file output	Output file for short summary in TXT format.
--full_table	file output	Full table output in TSV format.
--missing_busco_list	file output	Missing list output in TSV format.
--output_dir	file output	The full output directory, if so desired.

Name

Type & Properties

--short_summary_json

file

output

--short_summary_txt

file

output

--full_table

file

output

--missing_busco_list

file

output

--output_dir

file

output

Resource and Run Settings

Name	Type & Properties	Description
--force	boolean_true	Force rewriting of existing files. Must be used when output files with the provided name already exist.
--quiet -q	boolean_true	Disable the info logs, displays only errors.
--restart -r	boolean_true	Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.
--tar	boolean_true	Compress some subdirectories with many files to save space.

Name

Type & Properties

--force

boolean_true

--quiet

-q

boolean_true

--restart

-r

boolean_true

--tar

boolean_true

Lineage Dataset Settings

Name	Type & Properties	Description
--auto_lineage	boolean_true	Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.
--auto_lineage_euk	boolean_true	Run auto-placement just on eukaryota tree to find optimal lineage path.
--auto_lineage_prok	boolean_true	Run auto_lineage just on prokaryota trees to find optimum lineage path.
--datasets_version	string	Specify the version of BUSCO datasets

Name

Type & Properties

--auto_lineage

boolean_true

--auto_lineage_euk

boolean_true

--auto_lineage_prok

boolean_true

--datasets_version

string

Augustus Settings

Name	Type & Properties	Description
--augustus	boolean_true	Use augustus gene predictor for eukaryote runs.
--augustus_parameters	string	Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md). Parameters should be contained within a single string, without whitespace and seperated by commas.
--augustus_species	string	Specify the augustus species
--long	boolean_true	Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.

Name

Type & Properties

--augustus

boolean_true

--augustus_parameters

string

--augustus_species

string

--long

boolean_true

BBTools Settings

Name	Type & Properties	Description
--contig_break	integer	Number of contiguous Ns to signify a break between contigs in BBTools analysis.
--limit	integer	Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO. This option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.
--scaffold_composition	boolean_true	Writes ACGTN content per scaffold to a file scaffold_composition.txt.

Name

Type & Properties

--contig_break

integer

--limit

integer

--scaffold_composition

boolean_true

BLAST Settings

Name	Type & Properties	Description
--e_value	double	E-value cutoff for BLAST searches.

Name

Type & Properties

--e_value

double

Protein Gene Prediction settings

Name	Type & Properties	Description
--miniprot	boolean_true	Use Miniprot gene predictor.

Name

Type & Properties

--miniprot

boolean_true

MetaEuk Settings

Name	Type & Properties	Description
--metaeuk	boolean_true	Use Metaeuk gene predictor.
--metaeuk_parameters	string	Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk). All parameters should be contained within a single string with no white space, with each parameter separated by a comma.
--metaeuk_rerun_parameters	string	Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk). All parameters should be contained within a single string with no white space, with each parameter separated by a comma.

Name

Type & Properties

--metaeuk

boolean_true

--metaeuk_parameters

string

--metaeuk_rerun_parameters

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
short_summary_json: "$id.$key.short_summary_json.json"  
short_summary_txt: "$id.$key.short_summary_txt.txt"  
full_table: "$id.$key.full_table.tsv"  
missing_busco_list: "$id.$key.missing_busco_list.tsv"  
output_dir: "$id.$key.output_dir.output_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/busco/busco_run/main.nf \  
  -params-file params.yaml

busco/busco_run

Inputs

Outputs

Resource and Run Settings

Lineage Dataset Settings

Augustus Settings

BBTools Settings

BLAST Settings

Protein Gene Prediction settings

MetaEuk Settings

Run this component

Relationships

Used by

Uses