Command line interface reference
BEDboss is command-line tool-manager and a set of tools for working with BED files and BEDbase. Main components of BEDboss are: 1) Pipeline for processing BED files: bedmaker, bedqc, and bedstats. 2) Indexing of the Bed files in bedbase 3) Managing bed and bedsets in the database
Here you can see the command-line usage instructions for the main bedboss command and for each subcommand:
bedboss --help
Usage: bedboss [OPTIONS] COMMAND [ARGS]...
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --version -v App version │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or │
│ customize the installation. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────╮
│ run-all Run all the bedboss pipeline for a single bed file │
│ run-pep Run the all bedboss pipeline for a bed files in a PEP │
│ reprocess-all Run unprocessed files, or reprocess them │
│ reprocess-one Run unprocessed file, or reprocess it [Only 1 file] │
│ reprocess-bedset Reprocess a bedset │
│ make-bed Create a bed files form a [bigwig, bedgraph, bed, bigbed, │
│ wig] file │
│ make-bigbed Create a bigbed files form a bed file │
│ run-qc Run the quality control for a bed file │
│ run-stats Create the statistics for a single bed file. │
│ reindex Reindex the bedbase database and insert all files to the │
│ qdrant database. │
│ make-bedset Create a bedset from a pep file, and insert it to the bedbase │
│ database. │
│ init-config Initialize the new, sample configuration file │
│ delete-bed Delete bed from the bedbase database │
│ delete-bedset Delete BedSet from the bedbase database │
│ tokenize-bed Tokenize a bedfile │
│ delete-tokenized Delete tokenized bed file │
│ convert-universe Convert bed file to universe │
│ check-requirements Check installed R packages │
│ install-requirements Install R dependencies │
│ verify-config Verify configuration file │
│ geo Automatic BEDbase uploader for GEO data │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss geo --help
Usage: bedboss geo [OPTIONS] COMMAND [ARGS]...
Automatic BEDbase uploader for GEO data
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --version -v App version │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────╮
│ upload-all Run bedboss uploading pipeline for specified genome in specified period │
│ of time. │
│ upload-gse Run bedboss uploading pipeline for GSE. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss geo upload-all --help
Usage: bedboss geo upload-all [OPTIONS]
Run bedboss uploading pipeline for specified genome in specified period of time.
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to bedbase config │
│ file │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to output folder │
│ [default: None] │
│ [required] │
│ --start-date TEXT The earliest date when │
│ opep was updated │
│ [Default: 2000/01/01] │
│ [default: None] │
│ --end-date TEXT The latest date when opep │
│ was updated [Default: │
│ today's date] │
│ [default: None] │
│ --search-limit INTEGER Limit of projects to be │
│ searched. [Default: 50] │
│ [default: 50] │
│ --search-offset INTEGER Limit of projects to be │
│ searched. [Default: 0] │
│ [default: 0] │
│ --download-limit INTEGER Limit of projects to be │
│ downloaded [Default: 100] │
│ [default: 100] │
│ --genome TEXT Reference genome │
│ [Default: None] (e.g. │
│ hg38) - if None, all │
│ genomes will be processed │
│ [default: None] │
│ --preload --no-preload Download bedfile before │
│ caching it. [Default: │
│ True] │
│ [default: preload] │
│ --create-bedset --no-create-bedset Create bedset from bed │
│ files. [Default: True] │
│ [default: create-bedset] │
│ --overwrite --no-overwrite Overwrite existing │
│ bedfiles. [Default: │
│ False] │
│ [default: no-overwrite] │
│ --overwrite-bedset --no-overwrite-bedset Overwrite existing │
│ bedset. [Default: False] │
│ [default: │
│ overwrite-bedset] │
│ --rerun --no-rerun Re-run all the samples. │
│ [Default: False] │
│ [default: no-rerun] │
│ --run-skipped --no-run-skipped Run skipped projects. │
│ [Default: False] │
│ [default: run-skipped] │
│ --run-failed --no-run-failed Run failed projects. │
│ [Default: False] │
│ [default: run-failed] │
│ --standardize-pep --no-standardize-pep Standardize pep with │
│ BEDMESS. [Default: False] │
│ [default: │
│ no-standardize-pep] │
│ --use-skipper --no-use-skipper Use skipper to skip │
│ projects if they were │
│ processed locally │
│ [Default: False] │
│ [default: no-use-skipper] │
│ --reinit-skipper --no-reinit-skipper Reinitialize skipper. │
│ [Default: False] │
│ [default: │
│ no-reinit-skipper] │
│ --lite --no-lite Run the pipeline in lite │
│ mode. [Default: False] │
│ [default: no-lite] │
│ --help Show this message and │
│ exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss geo upload-gse --help
Usage: bedboss geo upload-gse [OPTIONS]
Run bedboss uploading pipeline for GSE.
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to bedbase config file │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to output folder │
│ [default: None] │
│ [required] │
│ * --gse TEXT GSE number that can be found │
│ in pephub. eg. GSE123456 │
│ [default: None] │
│ [required] │
│ --create-bedset --no-create-bedset Create bedset from bed │
│ files. [Default: True] │
│ [default: create-bedset] │
│ --genome TEXT reference genome to upload │
│ to database. If None, all │
│ genomes will be processed │
│ [default: None] │
│ --preload --no-preload Download bedfile before │
│ caching it. [Default: True] │
│ [default: preload] │
│ --rerun --no-rerun Re-run all the samples. │
│ [Default: False] │
│ [default: rerun] │
│ --run-skipped --no-run-skipped Run skipped projects. │
│ [Default: False] │
│ [default: run-skipped] │
│ --run-failed --no-run-failed Run failed projects. │
│ [Default: False] │
│ [default: run-failed] │
│ --overwrite --no-overwrite Overwrite existing bedfiles. │
│ [Default: False] │
│ [default: no-overwrite] │
│ --overwrite-bedset --no-overwrite-bedset Overwrite existing bedset. │
│ [Default: False] │
│ [default: overwrite-bedset] │
│ --standardize-pep --no-standardize-pep Standardize pep with │
│ BEDMESS. [Default: False] │
│ [default: │
│ no-standardize-pep] │
│ --use-skipper --no-use-skipper Use local skipper to skip │
│ projects if they were │
│ processed locally [Default: │
│ False] │
│ [default: no-use-skipper] │
│ --reinit-skipper --no-reinit-skipper Reinitialize skipper. │
│ [Default: False] │
│ [default: no-reinit-skipper] │
│ --lite --no-lite Run the pipeline in lite │
│ mode. [Default: False] │
│ [default: no-lite] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss run-all --help
Usage: bedboss run-all [OPTIONS]
Run all the bedboss pipeline for a single bed file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --input-file TEXT Path to the input file │
│ [default: None] │
│ [required] │
│ * --input-type TEXT Type of the input file. │
│ Options are: bigwig, │
│ bedgraph, bed, bigbed, wig │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ * --genome TEXT Genome name. Example: │
│ 'hg38' │
│ [default: None] │
│ [required] │
│ * --bedbase-config TEXT Path to the bedbase config │
│ file │
│ [default: None] │
│ [required] │
│ --license-id TEXT License ID. If not provided │
│ for in PEPfor each bed │
│ file, this license will be │
│ used │
│ [default: DUO:0000042] │
│ --rfg-config TEXT Path to the rfg config file │
│ [default: None] │
│ --narrowpeak --no-narrowpeak Is the input file a │
│ narrowpeak file? │
│ [default: no-narrowpeak] │
│ --check-qc --no-check-qc Check the quality of the │
│ input file? │
│ [default: check-qc] │
│ --chrom-sizes TEXT Path to the chrom sizes │
│ file │
│ [default: None] │
│ --open-signal-matrix TEXT Path to the open signal │
│ matrix file │
│ [default: None] │
│ --ensdb TEXT Path to the EnsDb database │
│ file │
│ [default: None] │
│ --just-db-commit --no-just-db-commit Just commit to the │
│ database? │
│ [default: │
│ no-just-db-commit] │
│ --force-overwrite --no-force-overwrite Force overwrite the output │
│ files │
│ [default: │
│ no-force-overwrite] │
│ --update --no-update Update the bedbase database │
│ with the new record if it │
│ exists. This overwrites │
│ 'force_overwrite' option │
│ [default: no-update] │
│ --lite --no-lite Run the pipeline in lite │
│ mode. [Default: False] │
│ [default: no-lite] │
│ --upload-qdrant --no-upload-qdrant Upload to Qdrant │
│ [default: no-upload-qdrant] │
│ --upload-s3 --no-upload-s3 Upload to S3 │
│ [default: no-upload-s3] │
│ --upload-pephub --no-upload-pephub Upload to PEPHub │
│ [default: no-upload-pephub] │
│ --universe --no-universe Create a universe │
│ [default: no-universe] │
│ --universe-method TEXT Method used to create the │
│ universe │
│ [default: None] │
│ --universe-bedset TEXT Bedset used used to create │
│ the universe │
│ [default: None] │
│ --multi --no-multi Run multiple samples │
│ [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing │
│ existing files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss run-pep --help
Usage: bedboss run-pep [OPTIONS]
Run the all bedboss pipeline for a bed files in a PEP
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --pep TEXT PEP file. Local or remote path │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ * --bedbase-config TEXT Path to the bedbase config │
│ file │
│ [default: None] │
│ [required] │
│ --create-bedset --no-create-bedset Create a new bedset │
│ [default: create-bedset] │
│ --bedset-heavy --no-bedset-heavy Run the heavy version of the │
│ bedbuncher pipeline │
│ [default: no-bedset-heavy] │
│ --bedset-id TEXT Bedset ID [default: None] │
│ --rfg-config TEXT Path to the rfg config file │
│ [default: None] │
│ --check-qc --no-check-qc Check the quality of the input │
│ file? │
│ [default: check-qc] │
│ --ensdb TEXT Path to the EnsDb database │
│ file │
│ [default: None] │
│ --just-db-commit --no-just-db-commit Just commit to the database? │
│ [default: no-just-db-commit] │
│ --force-overwrite --no-force-overwrite Force overwrite the output │
│ files │
│ [default: no-force-overwrite] │
│ --update --no-update Update the bedbase database │
│ with the new record if it │
│ exists. This overwrites │
│ 'force_overwrite' option │
│ [default: no-update] │
│ --upload-qdrant --no-upload-qdrant Upload to Qdrant │
│ [default: upload-qdrant] │
│ --upload-s3 --no-upload-s3 Upload to S3 │
│ [default: upload-s3] │
│ --upload-pephub --no-upload-pephub Upload to PEPHub │
│ [default: upload-pephub] │
│ --no-fail --no-no-fail Do not fail on error │
│ [default: no-no-fail] │
│ --license-id TEXT License ID │
│ [default: DUO:0000042] │
│ --standardize-pep --no-standardize-pep Standardize the PEP using │
│ bedMS │
│ [default: no-standardize-pep] │
│ --lite --no-lite Run the pipeline in lite mode. │
│ [Default: False] │
│ [default: no-lite] │
│ --rerun --no-rerun Rerun already processed │
│ samples │
│ [default: no-rerun] │
│ --multi --no-multi Run multiple samples │
│ [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing existing │
│ files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss reprocess-all --help
Usage: bedboss reprocess-all [OPTIONS]
Run unprocessed files, or reprocess them
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to the bedbase config file │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ --limit INTEGER Limit the number of files to │
│ reprocess │
│ [default: 100] │
│ --no-fail --no-no-fail Do not fail on error │
│ [default: no-fail] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss reprocess-one --help
Usage: bedboss reprocess-one [OPTIONS]
Run unprocessed file, or reprocess it [Only 1 file]
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to the bedbase config file [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder [default: None] │
│ [required] │
│ * --identifier TEXT Identifier of the bed file [default: None] │
│ [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss reprocess-bedset --help
Usage: bedboss reprocess-bedset [OPTIONS]
Reprocess a bedset
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to the bedbase config file │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ * --identifier TEXT Bedset ID [default: None] [required] │
│ --no-fail --no-no-fail Do not fail on error [default: no-fail] │
│ --heavy --no-heavy Run the heavy version of the pipeline │
│ [default: no-heavy] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss make-bed --help
Usage: bedboss make-bed [OPTIONS]
Create a bed files form a [bigwig, bedgraph, bed, bigbed, wig] file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --input-file TEXT Path to the input file [default: None] │
│ [required] │
│ * --input-type TEXT Type of the input file. Options are: │
│ bigwig, bedgraph, bed, bigbed, wig │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ * --genome TEXT Genome name. Example: 'hg38' │
│ [default: None] │
│ [required] │
│ --rfg-config TEXT Path to the rfg config file │
│ [default: None] │
│ --narrowpeak --no-narrowpeak Is the input file a narrowpeak file? │
│ [default: no-narrowpeak] │
│ --chrom-sizes TEXT Path to the chrom sizes file │
│ [default: None] │
│ --multi --no-multi Run multiple samples │
│ [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing existing files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss make-bigbed --help
Usage: bedboss make-bigbed [OPTIONS]
Create a bigbed files form a bed file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bed-file TEXT Path to the input file [default: None] │
│ [required] │
│ * --bed-type TEXT bed type to be used for bigBed file │
│ generation 'bed{bedtype}+{n}' [Default: │
│ None] (e.g bed3+1) │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder [default: None] │
│ [required] │
│ * --genome TEXT Genome name. Example: 'hg38' │
│ [default: None] │
│ [required] │
│ --rfg-config TEXT Path to the rfg config file │
│ [default: None] │
│ --chrom-sizes TEXT Path to the chrom sizes file │
│ [default: None] │
│ --multi --no-multi Run multiple samples [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing existing files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss run-qc --help
Usage: bedboss run-qc [OPTIONS]
Run the quality control for a bed file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bed-file TEXT Path to the bed file to check the │
│ quality control on. │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ --max-file-size INTEGER Maximum file size threshold to │
│ pass the quality │
│ [default: 2147483648] │
│ --max-region-number INTEGER Maximum number of regions │
│ threshold to pass the quality │
│ [default: 5000000] │
│ --min-region-width INTEGER Minimum region width threshold to │
│ pass the quality │
│ [default: 10] │
│ --multi --no-multi Run multiple samples │
│ [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing existing │
│ files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss run-stats --help
Usage: bedboss run-stats [OPTIONS]
Create the statistics for a single bed file.
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bed-file TEXT Path to the bed file │
│ [default: None] │
│ [required] │
│ * --genome TEXT Genome name. Example: 'hg38' │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ --ensdb TEXT Path to the EnsDb database │
│ file │
│ [default: None] │
│ --open-signal-matrix TEXT Path to the open signal │
│ matrix file │
│ [default: None] │
│ --just-db-commit --no-just-db-commit Just commit to the database? │
│ [default: no-just-db-commit] │
│ --multi --no-multi Run multiple samples │
│ [default: no-multi] │
│ --recover --no-recover Recover from previous run │
│ [default: recover] │
│ --dirty --no-dirty Run without removing │
│ existing files │
│ [default: no-dirty] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss reindex --help
Usage: bedboss reindex [OPTIONS]
Reindex the bedbase database and insert all files to the qdrant database.
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bedbase-config TEXT Path to the bedbase config file [default: None] │
│ [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss make-bedset --help
Usage: bedboss make-bedset [OPTIONS]
Create a bedset from a pep file, and insert it to the bedbase database.
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --pep TEXT PEP file. Local or remote path │
│ [default: None] │
│ [required] │
│ * --outfolder TEXT Path to the output folder │
│ [default: None] │
│ [required] │
│ * --bedbase-config TEXT Path to the bedbase config │
│ file │
│ [default: None] │
│ [required] │
│ * --bedset-name TEXT Name of the bedset │
│ [default: None] │
│ [required] │
│ --heavy --no-heavy Run the heavy version of the │
│ pipeline │
│ [default: no-heavy] │
│ --force-overwrite --no-force-overwrite Force overwrite the output │
│ files │
│ [default: no-force-overwrite] │
│ --upload-s3 --no-upload-s3 Upload to S3 │
│ [default: no-upload-s3] │
│ --upload-pephub --no-upload-pephub Upload to PEPHub │
│ [default: no-upload-pephub] │
│ --no-fail --no-no-fail Do not fail on error │
│ [default: no-no-fail] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss init-config --help
Usage: bedboss init-config [OPTIONS]
Initialize the new, sample configuration file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --outfolder TEXT Path to the output folder [default: None] [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss delete-bed --help
Usage: bedboss delete-bed [OPTIONS]
Delete bed from the bedbase database
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --sample-id TEXT Sample ID [default: None] [required] │
│ * --config TEXT Path to the bedbase config file [default: None] │
│ [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss delete-bedset --help
Usage: bedboss delete-bedset [OPTIONS]
Delete BedSet from the bedbase database
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --identifier TEXT BedSet ID [default: None] [required] │
│ * --config TEXT Path to the bedbase config file [default: None] │
│ [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss tokenize-bed --help
Usage: bedboss tokenize-bed [OPTIONS]
Tokenize a bedfile
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bed-id TEXT Path to the bed file [default: None] │
│ [required] │
│ * --universe-id TEXT Universe ID [default: None] │
│ [required] │
│ --cache-folder TEXT Path to the cache folder │
│ [default: None] │
│ --add-to-db --no-add-to-db Add the tokenized bed file to the │
│ bedbase database │
│ [default: no-add-to-db] │
│ --bedbase-config TEXT Path to the bedbase config file │
│ [default: None] │
│ --overwrite --no-overwrite Overwrite the existing tokenized bed │
│ file │
│ [default: no-overwrite] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss delete-tokenized --help
Usage: bedboss delete-tokenized [OPTIONS]
Delete tokenized bed file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --universe-id TEXT Universe ID [default: None] [required] │
│ * --bed-id TEXT Bed ID [default: None] [required] │
│ --config TEXT Path to the bedbase config file [default: None] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss convert-universe --help
Usage: bedboss convert-universe [OPTIONS]
Convert bed file to universe
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --bed-id TEXT Path to the bed file [default: None] [required] │
│ * --config TEXT Path to the bedbase config file [default: None] [required] │
│ --method TEXT Method used to create the universe [default: None] │
│ --bedset TEXT Bedset used to create the universe [default: None] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss check-requirements --help
Usage: bedboss check-requirements [OPTIONS]
Check installed R packages
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss install-requirements --help
Usage: bedboss install-requirements [OPTIONS]
Install R dependencies
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss verify-config --help
Usage: bedboss verify-config [OPTIONS]
Verify configuration file
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ * --config TEXT Path to the bedbase config file [default: None] [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bedboss get-commands --help
Usage: bedboss get-commands [OPTIONS]
Get available commands
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯