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bugfix fetch_sra_to_bam #542

Merged
merged 9 commits into from
Jun 19, 2024
Merged

bugfix fetch_sra_to_bam #542

merged 9 commits into from
Jun 19, 2024

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tomkinsc
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bugfix fetch_sra_to_bam task; API changes:

  • specify -db sra for efetch call
  • change -q to -query for esearch call

Changes to be a better user of the NCBI API:

  • set the NCBI_API_KEY environment variable if a value is passed in as a task input
  • pass a user email address to esearch and efetch calls via the -email param (not necessary when an API key is used, but easy to obtain through introspection on Terra—if running on Terra—for users without an NCBI API key)

@tomkinsc tomkinsc merged commit 9f43dde into master Jun 19, 2024
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@tomkinsc tomkinsc deleted the ct-bugifx-sra-fetch branch June 19, 2024 22:39
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