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  1. UGENE
  2. UGENE-6118

Adapters file for Trimmomatic on Windows

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: master
    • Fix Version/s: 1.31
    • Component/s: NGS, Workflow
    • Labels:
      None
    • Environment:

      Windows

    • Story Points:
      5
    • Epic Link:
    • Sprint:
      DEV-31-2, DEV-31-3
    • Affect Type:
      Userdefined

      Description

      Currently a full path is specified for an adapters file parameter in the "ILLUMINACLIP" step of Trimmomatic. Different parameters are separated by ':'. This causes a problem when launching Trimmomatic on Windows, as the adapters file path contains ':' (e.g. "D:\path\TruSeq3-PE.fa"):

      Subtask {Trimmomatic tool} is failed: at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

      Copy an adapters file to the corresponding workflow folder and specify a relative path to the file in the Trimmomatic command.

        Attachments

          Issue Links

          relates to

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-6167 Do not output Trimmomatic adapters to the workflow output folder

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

            Activity

              People

              Assignee:
              kir Kirill Rasputin
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: