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Revert --batch change for pipeline_job.sh #327

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holtgrewe opened this issue Jan 10, 2023 · 1 comment · Fixed by #333
Closed

Revert --batch change for pipeline_job.sh #327

holtgrewe opened this issue Jan 10, 2023 · 1 comment · Fixed by #333

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@holtgrewe
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Is your feature request related to a problem? Please describe.
One cannot run multiple batches at the same time (the input of a batch may overlap, of course).

Describe the solution you'd like
Remove change to pipeline_job.sh again. Rather, allow to specify an optional SNAPPY_BATCH.

Describe alternatives you've considered
N/A

Additional context
N/A

@holtgrewe
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We can use the following snippet:

# Allow selection of batch
if [[ ! -z "${SNAPPY_BATCH-}" ]]; then
    SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}"
else
    SNAKEMAKE_BATCH_ARG=
fi

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