Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-6384

Extension of the default output file of the "Filter BAM/SAM files" workflow element and other issues

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: 1.31.1
    • Fix Version/s: None
    • Component/s: NGS, Workflow
    • Labels:
    • Affect Type:
      Userdefined

      Description

      Scenario:

      1. Open the Workflow Designer.
      2. Create the following workflow: "Read File URL(s) > Filter BAM/SAM files".
      3. Select the "Read File URL(s)" element, add an appropriate input SAM or BAM file.
      4. Select the "Filter BAM/SAM files" element. Set "Output format" to "sam".
      5. Run the workflow.
        Current result: the output file name is generated based on the input file name as follows: "filename.filtered.bam". Here filename also contains the input file extension.
        Expected result: TODO

      The following should be fixed:

      1. Rename the element from "Filter BAM/SAM files" to "Filter BAM/SAM Files" ('F' character should be uppercase).
      2. Correct the list of values of the "Output format" parameter. The values should be uppercase: SAM, BAM.
      3. Correct the output file extension in case of "SAM" output format (see the scenario above).

        Attachments

          Activity

            People

            Assignee:
            Unassigned
            Reporter:
            oigl Olga Golosova
            Watchers:
            0 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: