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  1. IGB
  2. IGBF-3348

Create sample sheet with SRA names for mature pollen and seedling dataset

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24

          Description

          Now that our pollen and seedling data are submitted to SRA, we are planning to download and re-run our nf-core rnaseq pipeline on the data as it exists in the SRA. Then, we will deploy the newly re-run data to IGB Quickload for users to view and explore. To re-deploy the data we need a new sample sheet that uses SRA names instead of our project-specific names.

          For this task, create a new sample spreadsheet named for the project name which uses the new SRA names.

          See the linked ticket IGBF-3254 for a mapping between original fastq file names and new SRA names.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3254 Submit Johnson lab mature pollen and tomato seedling data to SRA

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3254 [ IGBF-3254 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3347 [ IGBF-3347 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29 [ 171 ] Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Attachment seedlingPollen_sample_sheet.xlsx [ 17902 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Attachment seedlingPollen_sample_sheet.xlsx [ 17902 ]
                Mdavis4290 Molly Davis made changes -
                Attachment seedlingPollen_sample_sheet.xlsx [ 17903 ]
                Mdavis4290 Molly Davis made changes -
                Attachment seedlingPollen_sample_sheet.xlsx [ 17903 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ] Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ] Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10 [ 171, 172, 173, 174 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10 [ 171, 172, 173, 174 ] Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24 [ 171, 172, 173, 174, 175 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: