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SRA_fetch workflow & fastq-dl task improvements #150

Merged
merged 6 commits into from
Aug 23, 2023
Merged

SRA_fetch workflow & fastq-dl task improvements #150

merged 6 commits into from
Aug 23, 2023

Commits on Aug 10, 2023

  1. fastq-dl changes: update default docker to v2.0.3; default options ar… 

    …e to only download from SRA (instead of ENA); capture date and output as string; fastq-dl is always verbose; added --cpus option to cmd; added string outputs for fastq-dl version, docker image, and date it was run; added maxRetries to runtime block.
    @kapsakcj
    kapsakcj committed Aug 10, 2023
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  2. added new file output to fastq-dl task and sra_fetch wf: fastq metada… 

    …ta TSV
    @kapsakcj
    kapsakcj committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. update fastq-dl docker to 2.0.4 due to version mismatch issue with v2… 

    ….0.3
    @kapsakcj
    kapsakcj committed Aug 11, 2023
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Commits on Aug 21, 2023

  1. added fastq-dl --prefix flag; adjusted output filename to match

    @kapsakcj
    kapsakcj committed Aug 21, 2023
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  2. remove "--only-provider" from fastq-dl default options

    @kapsakcj
    kapsakcj committed Aug 21, 2023
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  3. deleted old code

    @kapsakcj
    kapsakcj committed Aug 21, 2023
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