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* config file and test data * organize config in argument groups and add script * add busco help text * add tests * add examples to config * add version script * Update src/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/script.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/script.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update version * add script to obtain test data * add changelog entry * Delete src/busco/version.sh * update cpus input * Update src/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * fix version * Update src/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/script.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/script.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * move into separate module * merge * add outputs * update tests * remove download flags - to be a separate component * modify description of list dataset * fix tests * remove files new comp * remove defaults * Update src/busco/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/busco/script.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * fix typo * remove unrequired params * remove unused vars * opt out of run stats by default * update tests * update test * remove directory level * add mkdir * enable copying from symlink * remove sleep command * Update src/busco/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/test.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/busco/test.sh Co-authored-by: Robrecht Cannoodt <[email protected]> * add output tests * fix typo * add genome test data and script * fix typo * typo * use smaller genome --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
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| functionality: | ||
| name: busco | ||
| description: Assessment of genome assembly and annotation completeness with single copy orthologs | ||
| info: | ||
| keywords: [Genome assembly, quality control] | ||
| homepage: https://busco.ezlab.org/ | ||
| documentation: https://busco.ezlab.org/busco_userguide.html | ||
| repository: https://gitlab.com/ezlab/busco | ||
| reference: "10.1007/978-1-4939-9173-0_14" | ||
| licence: MIT | ||
| argument_groups: | ||
| - name: Inputs | ||
| arguments: | ||
| - name: --input | ||
| alternatives: ["-i"] | ||
| type: file | ||
| description: | | ||
| 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. | ||
| required: true | ||
| example: file.fasta | ||
| - name: --mode | ||
| alternatives: ["-m"] | ||
| type: string | ||
| choices: [genome, geno, transcriptome, tran, proteins, prot] | ||
| required: true | ||
| description: | | ||
| 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) | ||
| example: proteins | ||
| - name: --lineage_dataset | ||
| alternatives: ["-l"] | ||
| type: string | ||
| required: false | ||
| description: | | ||
| 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 `busco --list-datasets` (which requires installing the tool). | ||
| When unsure, the "--auto_lineage" flag can be set to automatically find the optimal lineage path. | ||
| Requested datasets will automatically be downloaded if not already present in the download folder. | ||
| example: stramenopiles_odb10 | ||
|
|
||
| - name: Outputs | ||
| arguments: | ||
| - name: --short_summary_json | ||
| required: false | ||
| direction: output | ||
| type: file | ||
| example: short_summary.json | ||
| description: | | ||
| Output file for short summary in JSON format. | ||
| - name: --short_summary_txt | ||
| required: false | ||
| direction: output | ||
| type: file | ||
| example: short_summary.txt | ||
| description: | | ||
| Output file for short summary in TXT format. | ||
| - name: --full_table | ||
| required: false | ||
| direction: output | ||
| type: file | ||
| example: full_table.tsv | ||
| description: | | ||
| Full table output in TSV format. | ||
| - name: --missing_busco_list | ||
| required: false | ||
| direction: output | ||
| type: file | ||
| example: missing_busco_list.tsv | ||
| description: | | ||
| Missing list output in TSV format. | ||
| - name: --output_dir | ||
| required: false | ||
| direction: output | ||
| type: file | ||
| example: output_dir/ | ||
| description: | | ||
| The full output directory, if so desired. | ||
| - name: Resource and Run Settings | ||
| arguments: | ||
| - name: --force | ||
| type: boolean_true | ||
| description: | | ||
| Force rewriting of existing files. Must be used when output files with the provided name already exist. | ||
| - name: --quiet | ||
| alternatives: ["-q"] | ||
| type: boolean_true | ||
| description: | | ||
| Disable the info logs, displays only errors. | ||
| - name: --restart | ||
| alternatives: ["-r"] | ||
| type: boolean_true | ||
| description: | | ||
| Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps. | ||
| - name: --tar | ||
| type: boolean_true | ||
| description: | | ||
| Compress some subdirectories with many files to save space. | ||
| - name: Lineage Dataset Settings | ||
| arguments: | ||
| - name: --auto_lineage | ||
| type: boolean_true | ||
| description: | | ||
| Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. | ||
| - name: --auto_lineage_euk | ||
| type: boolean_true | ||
| description: | | ||
| Run auto-placement just on eukaryota tree to find optimal lineage path. | ||
| - name: --auto_lineage_prok | ||
| type: boolean_true | ||
| description: | | ||
| Run auto_lineage just on prokaryota trees to find optimum lineage path. | ||
| - name: --datasets_version | ||
| type: string | ||
| required: false | ||
| description: | | ||
| Specify the version of BUSCO datasets | ||
| example: odb10 | ||
|
|
||
| - name: Augustus Settings | ||
| arguments: | ||
| - name: --augustus | ||
| type: boolean_true | ||
| description: | | ||
| Use augustus gene predictor for eukaryote runs. | ||
| - name: --augustus_parameters | ||
| type: string | ||
| required: false | ||
| description: | | ||
| 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. | ||
| example: "--PARAM1=VALUE1,--PARAM2=VALUE2" | ||
| - name: --augustus_species | ||
| type: string | ||
| required: false | ||
| description: | | ||
| Specify the augustus species | ||
| - name: --long | ||
| type: boolean_true | ||
| description: | | ||
| Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms. | ||
| - name: BBTools Settings | ||
| arguments: | ||
| - name: --contig_break | ||
| type: integer | ||
| required: false | ||
| description: | | ||
| Number of contiguous Ns to signify a break between contigs in BBTools analysis. | ||
| - name: --limit | ||
| type: integer | ||
| required: false | ||
| description: | | ||
| 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. | ||
| - name: --scaffold_composition | ||
| type: boolean_true | ||
| description: | | ||
| Writes ACGTN content per scaffold to a file scaffold_composition.txt. | ||
| - name: BLAST Settings | ||
| arguments: | ||
| - name: --e_value | ||
| type: double | ||
| required: false | ||
| description: | | ||
| E-value cutoff for BLAST searches. | ||
| - name: Protein Gene Prediction settings | ||
| arguments: | ||
| - name: --miniprot | ||
| type: boolean_true | ||
| description: | | ||
| Use Miniprot gene predictor. | ||
| - name: MetaEuk Settings | ||
| arguments: | ||
| - name: --metaeuk_parameters | ||
| type: string | ||
| description: | | ||
| 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. | ||
| example: "--max-overlap=15,--min-exon-aa=15" | ||
| - name: --metaeuk_rerun_parameters | ||
| type: string | ||
| description: | | ||
| 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. | ||
| example: "--max-overlap=15,--min-exon-aa=15" | ||
|
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||
| resources: | ||
| - type: bash_script | ||
| path: script.sh | ||
| test_resources: | ||
| - type: bash_script | ||
| path: test.sh | ||
| - type: file | ||
| path: test_data | ||
| platforms: | ||
| - type: docker | ||
| image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 | ||
| setup: | ||
| - type: docker | ||
| run: | | ||
| busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt | ||
| - type: nextflow |
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| ```bash | ||
| busco -h | ||
| ``` | ||
|
|
||
| Welcome to BUSCO 5.6.1: the Benchmarking Universal Single-Copy Ortholog assessment tool. | ||
| For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO | ||
|
|
||
| optional arguments: | ||
| -i SEQUENCE_FILE, --in SEQUENCE_FILE | ||
| 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. | ||
| -o OUTPUT, --out OUTPUT | ||
| Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. The path to the output folder is set with --out_path. | ||
| -m MODE, --mode MODE 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) | ||
| -l LINEAGE, --lineage_dataset LINEAGE | ||
| Specify the name of the BUSCO lineage to be used. | ||
| --augustus Use augustus gene predictor for eukaryote runs | ||
| --augustus_parameters --PARAM1=VALUE1,--PARAM2=VALUE2 | ||
| Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma. | ||
| --augustus_species AUGUSTUS_SPECIES | ||
| Specify a species for Augustus training. | ||
| --auto-lineage Run auto-lineage to find optimum lineage path | ||
| --auto-lineage-euk Run auto-placement just on eukaryote tree to find optimum lineage path | ||
| --auto-lineage-prok Run auto-lineage just on non-eukaryote trees to find optimum lineage path | ||
| -c N, --cpu N Specify the number (N=integer) of threads/cores to use. | ||
| --config CONFIG_FILE Provide a config file | ||
| --contig_break n Number of contiguous Ns to signify a break between contigs. Default is n=10. | ||
| --datasets_version DATASETS_VERSION | ||
| Specify the version of BUSCO datasets, e.g. odb10 | ||
| --download [dataset [dataset ...]] | ||
| Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus". If used together with other command line arguments, make sure to place this last. | ||
| --download_base_url DOWNLOAD_BASE_URL | ||
| Set the url to the remote BUSCO dataset location | ||
| --download_path DOWNLOAD_PATH | ||
| Specify local filepath for storing BUSCO dataset downloads | ||
| -e N, --evalue N E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03) | ||
| -f, --force Force rewriting of existing files. Must be used when output files with the provided name already exist. | ||
| -h, --help Show this help message and exit | ||
| --limit N How many candidate regions (contig or transcript) to consider per BUSCO (default: 3) | ||
| --list-datasets Print the list of available BUSCO datasets | ||
| --long Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms | ||
| --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" | ||
| Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. | ||
| --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" | ||
| Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. | ||
| --miniprot Use miniprot gene predictor | ||
| --skip_bbtools Skip BBTools for assembly statistics | ||
| --offline To indicate that BUSCO cannot attempt to download files | ||
| --opt-out-run-stats Opt out of data collection. Information on the data collected is available in the user guide. | ||
| --out_path OUTPUT_PATH | ||
| Optional location for results folder, excluding results folder name. Default is current working directory. | ||
| -q, --quiet Disable the info logs, displays only errors | ||
| -r, --restart Continue a run that had already partially completed. | ||
| --scaffold_composition | ||
| Writes ACGTN content per scaffold to a file scaffold_composition.txt | ||
| --tar Compress some subdirectories with many files to save space | ||
| -v, --version Show this version and exit |
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| #!/bin/bash | ||
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| ## VIASH START | ||
| ## VIASH END | ||
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| [[ "$par_tar" == "false" ]] && unset par_tar | ||
| [[ "$par_force" == "false" ]] && unset par_force | ||
| [[ "$par_quiet" == "false" ]] && unset par_quiet | ||
| [[ "$par_restart" == "false" ]] && unset par_restart | ||
| [[ "$par_auto_lineage" == "false" ]] && unset par_auto_lineage | ||
| [[ "$par_auto_lineage_euk" == "false" ]] && unset par_auto_lineage_euk | ||
| [[ "$par_auto_lineage_prok" == "false" ]] && unset par_auto_lineage_prok | ||
| [[ "$par_augustus" == "false" ]] && unset par_augustus | ||
| [[ "$par_long" == "false" ]] && unset par_long | ||
| [[ "$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition | ||
| [[ "$par_miniprot" == "false" ]] && unset par_miniprot | ||
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| tmp_dir=$(mktemp -d -p "$meta_temp_dir" busco_XXXXXXXXX) | ||
| prefix=$(openssl rand -hex 8) | ||
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| busco \ | ||
| --in "$par_input" \ | ||
| --mode "$par_mode" \ | ||
| --out "$prefix" \ | ||
| --out_path "$tmp_dir" \ | ||
| --opt-out-run-stats \ | ||
| ${meta_cpus:+--cpu "${meta_cpus}"} \ | ||
| ${par_lineage_dataset:+--lineage_dataset "$par_lineage_dataset"} \ | ||
| ${par_augustus:+--augustus} \ | ||
| ${par_augustus_parameters:+--augustus_parameters "$par_augustus_parameters"} \ | ||
| ${par_augustus_species:+--augustus_species "$par_augustus_species"} \ | ||
| ${par_auto_lineage:+--auto-lineage} \ | ||
| ${par_auto_lineage_euk:+--auto-lineage-euk} \ | ||
| ${par_auto_lineage_prok:+--auto-lineage-prok} \ | ||
| ${par_contig_break:+--contig_break $par_contig_break} \ | ||
| ${par_datasets_version:+--datasets_version "$par_datasets_version"} \ | ||
| ${par_e_value:+--evalue "$par_e_value"} \ | ||
| ${par_force:+--force} \ | ||
| ${par_limit:+--limit "$par_limit"} \ | ||
| ${par_long:+--long} \ | ||
| ${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \ | ||
| ${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \ | ||
| ${par_miniprot:+--miniprot} \ | ||
| ${par_quiet:+--quiet} \ | ||
| ${par_restart:+--restart} \ | ||
| ${par_scaffold_composition:+--scaffold_composition} \ | ||
| ${par_tar:+--tar} \ | ||
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| out_dir=$(find "$tmp_dir/$prefix" -maxdepth 1 -name 'run_*') | ||
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| if [[ -n "$par_short_summary_json" ]]; then | ||
| cp "$out_dir/short_summary.json" "$par_short_summary_json" | ||
| fi | ||
| if [[ -n "$par_short_summary_txt" ]]; then | ||
| cp "$out_dir/short_summary.txt" "$par_short_summary_txt" | ||
| fi | ||
| if [[ -n "$par_full_table" ]]; then | ||
| cp "$out_dir/full_table.tsv" "$par_full_table" | ||
| fi | ||
| if [[ -n "$par_missing_busco_list" ]]; then | ||
| cp "$out_dir/missing_busco_list.tsv" "$par_missing_busco_list" | ||
| fi | ||
| if [[ -n "$par_output_dir" ]]; then | ||
| if [[ -d "$par_output_dir" ]]; then | ||
| rm -r "$par_output_dir" | ||
| fi | ||
| cp -r -L "$out_dir" "$par_output_dir" | ||
| fi | ||
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