How to upload BED files using PEP
1. Create PEP with BED files metadata
Section titled “1. Create PEP with BED files metadata”To upload BED files from PEP, first we should create a PEP project locally or on PEPhub.
PEP must include this fields in sample table:
- ✅ "sample_name"
- ✅ "input_file"
- ✅ "input_type"
- ✅ "genome"
ℹ️ All other fields are optional. Schema for PEP can be found here
ℹ️ All peps before their upload are validated against the schema using eido tool.
2. Make sure all paths or urls to input bed files are correct.
Section titled “2. Make sure all paths or urls to input bed files are correct.”To complete this step, you should manually check that all paths or urls to input bed files are correct.
3. Run bedboss upload command:
Section titled “3. Run bedboss upload command:”bedboss run-pep --pep <path_to_pep> --outfolder <path_to_output_folder> --bedbase-config <path_to_bedbase_config>Full bedboss run-pep help
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. │╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯