BEDboss-all pipeline

Bedboss run-all

Bedboss run-all is intended to run on ONE sample (bed file) and run all bedboss pipelines: bedmaker (+ bedclassifier + bedqc) -> bedstat. After that optionally it can run bedbuncher, qdrant indexing and upload metadata to PEPhub.

Step 1: Install all dependencies

First you have to install bedboss and check if all requirements are satisfied. To do so, you can run next command:

bedboss check-requirements

If requirements are not satisfied, you will see the list of missing packages.

Step 2: Create bedconf.yaml file

To run bedboss, you need to create a bedconf.yaml file with configuration. Detail instructions are in the configuration section.

Step 3: Run bedboss

To run bedboss, you need to run the next command:

bedboss all \
    --bedbase-config bedconf.yaml \
    --input-file path/to/bedfile.bed \
    --outfolder path/to/output/dir \
    --input-type bed \
    --genome hg38 \

Above command will run bedboss on the bed file and create a bedstat file in the output directory. It contains only required parameters. For more details, please check the usage section.

By default, results will be uploaded only to the PostgreSQL database.

• To upload results to PEPhub, you need to make the databio org available on GitHub, then login to PEPhub, and add the --upload-pephub flag to the command.
• To upload results to Qdrant, you need to add the --upload-qdrant flag to the command.
• To upload actual files to S3, you need to add the --upload-s3 flag to the command, and before uploading, you have to set up all necessary environment variables: AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, and AWS_ENDPOINT_URL.
• To ignore errors and continue processing, you need to add the --no-fail flag to the command.

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Run bedboss all from within Python

To run bedboss all from within Python, instead of using the command line in the step #3, you can use the following code:

from bedboss import bedboss

bedboss.run_all(
    name="sample1",
    input_file="path/to/bedfile.bed",
    input_type="bed",
    outfolder="path/to/output/dir",
    genome="hg38",
    bedbase_config="bedconf.yaml",
    other_metadata=None,  # optional
    upload_pephub=True,  # optional
    upload_qdrant=True,  # optional
    upload_s3=True,  # optional
)