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:
- Pipeline for processing BED files: bedmaker, bedqc, and bedstats.
- Indexing of the Bed files in bedbase
- 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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “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
Section titled “bedboss check-requirements --help” Usage: bedboss check-requirements [OPTIONS]
Check installed R packages
╭─ Options ────────────────────────────────────────────────────────────────────────────╮│ --help Show this message and exit. │╰──────────────────────────────────────────────────────────────────────────────────────╯bedboss install-requirements --help
Section titled “bedboss install-requirements --help” Usage: bedboss install-requirements [OPTIONS]
Install R dependencies
╭─ Options ────────────────────────────────────────────────────────────────────────────╮│ --help Show this message and exit. │╰──────────────────────────────────────────────────────────────────────────────────────╯bedboss verify-config --help
Section titled “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
Section titled “bedboss get-commands --help” Usage: bedboss get-commands [OPTIONS]
Get available commands
╭─ Options ────────────────────────────────────────────────────────────────────────────╮│ --help Show this message and exit. │╰──────────────────────────────────────────────────────────────────────────────────────╯