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  1. UGENE
  2. UGENE-6096

Dialog for configuring Trimmomatic steps: other steps

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: virogenesis
    • Fix Version/s: 1.31
    • Component/s: NGS, Workflow
    • Labels:
      None
    • Story Points:
      2
    • Epic Link:
    • Sprint:
      DEV-31-1, DEV-31-2
    • Affect Type:
      Userdefined

      Description

      Add a pop-up menu to the "Add step" button in the "Configure Trimmomatic Steps" dialog (see UGENE-6095). The menu should be opened on this button click and contain the following items:

      1. ILLUMINACLIP
      2. SLIDINGWINDOW
      3. MAXINFO
      4. LEADING
      5. TRAILING
      6. CROP
      7. HEADCROP
      8. MINLEN
      9. AVGQUAL
      10. TOPHRED33
      11. TOPHRED64

      When an item is selected, it should appear in the "Steps" list. The added item should be selected by default. The "Step settings" widget should be modified accordingly to the selected item (see below) as well as the descriptions widget (see "descritpions_other_steps.zip").

      Implement modification of the steps order in the list using the up and down buttons. Make sure the "Remove step" button works properly.

      If a user clicks on the "Apply" button in the dialog, a string with the correct order of steps should be generated, e.g. in the string "CROP:5 HEADCROP:4" the first step is CROP and the second step is HEADCROP. Note that it is possible to add the same step with different (or the same) parameters several times.

      See possible and default values for different settings below. The unset values should be highlighted in pink, the "Apply" button should be disabled in this case. Also highlight the background of the corresponding item in the list (also in pink).

      1. ILLUMINACLIP - should be already implemented in UGENE-6095.
      2. SLIDINGWINDOW
        • Window size: INT > 1, default - none.
        • Quality threshold: INT > 0, default - "20".
      3. MAXINFO
        • Target length: INT > 0, default - "40".
        • Strictness: DOUBLE > 0, <1, default - "0.5".
      4. LEADING
        • Quality threshold: INT > 0, default - "20".
      5. TRAILING
        • Quality threshold: INT > 0, default - "20".
      6. CROP
        • Length: INT > 0, default - none.
      7. HEADCROP
        • Length: INT > 0, default - none.
      8. MINLEN
        • Length: INT > 0, default - none.
      9. AVGQUAL
        • Quality threshold: INT > 0, default - "20".
      10. TOPHRED33 - show label "There are no settings for this step.".
      11. TOPHRED64 - show label "There are no settings for this step.".

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              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Svetlana Samoilenko
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                Dates

                Created:
                Updated:
                Resolved: