Methods and functions that support the overall operations of code based on Hail Batch.

Project description

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

Project details

Release history Release notifications | RSS feed

0.1.5.1

Mar 24, 2022

0.1.5

Mar 24, 2022

0.1.3

Mar 9, 2022

0.1.2

Feb 19, 2022

This version

0.1.1

Feb 1, 2022

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