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[MRG] add a flag to prevent metagenome download from SRA #157

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merged 11 commits into from
Feb 12, 2022
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@ctb ctb commented Feb 4, 2022

This PR adds a flag, prevent_sra_download, that when set to True makes the download_sra_wc rule break instead of embarking on expensive SRA downloads.

The output from the rule when it fails is messy but starts with:

** genome-grist is trying to download from SRA for sample SRR5950647,
** but 'prevent_sra_download' is set to true in config.
** Does 'outputs.test/abundtrim/SRR5950647.abundtrim.fq.gz' exist?

Fixes #152

@ctb ctb merged commit 72c44c9 into latest Feb 12, 2022
@ctb ctb deleted the add/prevent_sra branch February 12, 2022 18:26
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add a download_from_sra: flag in config file...
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