batchutils

Overview

Main Features

Installation

Usage

Use the following function as is. Replace the paths with [j1.ofile, j2.ofile, ...]

b = hb.Batch(
    default_image='hailgenetics/hail:0.2.77,
    backend=service_backend,
    name=f'combine-tsvs'
)
combined = batch_combine2(
    combine_tsvs_with_headers,
    combine_compressed_tsvs_with_headers,
    b,
    'combine-tsvs-with-headers',
    ['gs://bucket/input1.tsv', ...],
    final_location='gs://bucket/final-file.tsv.gz',
    branching_factor=25,
    suffix='.tsv.bgz')

final_location is where the output file is.

Cite

Maintainer

Tarjinder Singh @ tsingh@broadinstitute.org

Acknowledgements

Release Notes

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