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  1. UGENE
  2. UGENE-5835

Add “Classify Sequences with Kraken” workflow element

    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 1.28
    • Fix Version/s: 1.31
    • Component/s: NGS
    • Labels:
      None
    • Story Points:
      5
    • Epic Link:
    • Sprint:
      DEV-29-1, DEV-29-2, DEV-29-3
    • Affect Type:
      Userdefined

      Description

      Add the “Classify Sequences with Kraken” workflow element according to the specification.

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            atiunov Aleksey Tiunov [X] (Inactive) added a comment -

            The element can accept two URLs to files with reads. These URLs come from file list reads, where files to read are set separately. One can make a mistake and pass URLs to the readers in the incorrect order. Usually paired reads are in files with very close names. Maybe we should add a check that URLs are similar enough? In this case we can show a warning and continue reads processing.

            Show
            atiunov Aleksey Tiunov [X] (Inactive) added a comment - The element can accept two URLs to files with reads. These URLs come from file list reads, where files to read are set separately. One can make a mistake and pass URLs to the readers in the incorrect order. Usually paired reads are in files with very close names. Maybe we should add a check that URLs are similar enough? In this case we can show a warning and continue reads processing.
            Hide
            oigl Olga Golosova added a comment -

            Note that the output slot of the element should have type "Taxonomic classification", but the modification of the slot will be done in terms of UGENE-5893.

            Show
            oigl Olga Golosova added a comment - Note that the output slot of the element should have type "Taxonomic classification", but the modification of the slot will be done in terms of UGENE-5893 .
            Hide
            epushkova Eugenia Pushkova [X] (Inactive) added a comment -

            The element is not user-friendly:

            • user should setup slots manually instead of automatically match the right ones
            • if 'Input data' is set to 'SE reads or scaffolds', there are still two slots instead of one and the warning appears on the workflow run.
            • database setup is unclear - one cannot see the folders content
            Show
            epushkova Eugenia Pushkova [X] (Inactive) added a comment - The element is not user-friendly: user should setup slots manually instead of automatically match the right ones if 'Input data' is set to 'SE reads or scaffolds', there are still two slots instead of one and the warning appears on the workflow run. database setup is unclear - one cannot see the folders content
            Hide
            oigl Olga Golosova added a comment -

            user should setup slots manually instead of automatically match the right ones

            This has been fixed in terms of UGENE-6011.

            if 'Input data' is set to 'SE reads or scaffolds', there are still two slots instead of one and the warning appears on the workflow run.

            See UGENE-6038.

            database setup is unclear - one cannot see the folders content

            I mentioned this in UGENE-6039.

            Show
            oigl Olga Golosova added a comment - user should setup slots manually instead of automatically match the right ones This has been fixed in terms of UGENE-6011 . if 'Input data' is set to 'SE reads or scaffolds', there are still two slots instead of one and the warning appears on the workflow run. See UGENE-6038 . database setup is unclear - one cannot see the folders content I mentioned this in UGENE-6039 .
            Hide
            yalgaer Yuliya Algaer added a comment -

            Reviewed

            Show
            yalgaer Yuliya Algaer added a comment - Reviewed

              People

              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              atiunov Aleksey Tiunov [X] (Inactive)
              Assigned Tester:
              Eugenia Pushkova [X] (Inactive)
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: