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Parallelize download_reference rule #1064

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fevac opened this issue Jan 20, 2023 · 0 comments · Fixed by #1065
Closed

Parallelize download_reference rule #1064

fevac opened this issue Jan 20, 2023 · 0 comments · Fixed by #1065
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fevac commented Jan 20, 2023

Description

Currently all references are download one by one in a single rule which makes it not only slow but also painful when a reference file fails to download since the download has to be re-started from scratch.

It would be nice that the download rule would run independently for each reference file. Partially overlapping with what is suggested here: #1044

Suggested solution

  • Modify download_reference rule to be launched independently for each reference file

BALSAMIC version
11.0.2

Current affected rule if snakemake workflow related
download_reference
@fevac fevac changed the title Split download_reference rule Parallelize download_reference rule Jan 23, 2023
@fevac fevac mentioned this issue Jan 23, 2023
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@fevac fevac self-assigned this Jan 23, 2023
@fevac fevac linked a pull request Jan 23, 2023 that will close this issue
perf: Parallelize download reference #1065
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@fevac fevac mentioned this issue Jan 23, 2023
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@fevac fevac closed this as completed Feb 1, 2023
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perf: Parallelize download reference Clinical-Genomics/BALSAMIC
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