Code

bugfix fetch_sra_to_bam#542

Code

Merged

tomkinsc merged 9 commits intomasterbroadinstitute/viral-pipelines:masterfrom ct-bugifx-sra-fetchbroadinstitute/viral-pipelines:ct-bugifx-sra-fetchCopy head branch name to clipboardJun 19, 2024

+35-19

Commits

Commits on Jun 19, 2024

• in fetch_sra_to_bam, make json parsing of metadata more flexible in the possible return values it can process

  tomkinsc

  committed
  cf57b44

  Copy full SHA for cf57b44

• add email address and ncbi api key to inputs for Fetch_SRA_to_BAM; pass terra email from workflow (iff running on terra)

  tomkinsc

  committed
  952c9e7

  Copy full SHA for 952c9e7

• add braces

  tomkinsc

  committed
  7705580

  Copy full SHA for 7705580

• select_first email

  tomkinsc

  committed
  90dfb24

  Copy full SHA for 90dfb24

• array

  tomkinsc

  committed
  a579edb

  Copy full SHA for a579edb

• pass empty string

  tomkinsc

  committed
  600f121

  Copy full SHA for 600f121

• add '-db sra' to efetch call

  tomkinsc

  committed
  c44f1fd

  Copy full SHA for c44f1fd

• bump pinned docker versions; temporarily skip enforcement of version pinning for viral-classify in tasks_megablast.wdl

  tomkinsc

  committed
  6e6f2f6

  Copy full SHA for 6e6f2f6

• temporarily skip version pinning of viral-classify in tasks_megablast.wdl

  tomkinsc

  committed
  daa70c5

  Copy full SHA for daa70c5