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  1. IGB
  2. IGBF-3721

Document Tardigrade RNA-Seq Pipeline

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          The genomic pipeline for downloading and processing tomato data has been well documented, but it includes a version of Nextflow which has recently been superseded. Now that we're working on setting up tardigrade quickloads, we should ideally be adapting this pipeline to use the newest version of Nextflow. This pipeline will likely be shared with the Goldstein lab as part of our outreach efforts.

          Task: Document the genomic pipeline for downloading and processing tardigrade RNA-Seq data with the newest version of Nextflow. Ensure that it is easy to understand (i.e., keep the Goldstein lab in mind as a target audience).

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3735 Run the latest version of the nf-core/rnaseq pipeline with tardigrade data

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3790 Run nf-core/rnaseq v 3.14 on SRP484252 (2024 Goldstein Lab)

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3708 Download tardigrade RNA-Seq data onto cluster

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-1395 [ 17470 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3708 [ IGBF-3708 ]
                pkulzer Paige Kulzer made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9 [ 193 ] Spring 9, Spring 10 [ 193, 194 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Summary Document Genomic Pipeline for Tardigrades Document Tardigrade RNA-Seq Pipeline
                pkulzer Paige Kulzer made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3735 [ IGBF-3735 ]
                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 ] Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Sprint Spring 9, Spring 10 [ 193, 194 ] Spring 9, Summer 1 [ 193, 195 ]
                pkulzer Paige Kulzer made changes -
                Sprint Spring 9, Summer 1 [ 193, 195 ] Spring 9 [ 193 ]
                pkulzer Paige Kulzer made changes -
                Sprint Spring 9 [ 193 ] Spring 9, Summer 1 [ 193, 195 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 9, Summer 1 [ 193, 195 ] Spring 9 [ 193 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 9 [ 193 ] Spring 9, Summer 2 [ 193, 196 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1395 [ 17470 ] IGBF-3778 [ 22997 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9, Summer 2 [ 193, 196 ] Spring 9, Summer 2, Summer 3 [ 193, 196, 197 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9, Summer 2, Summer 3 [ 193, 196, 197 ] Spring 9, Summer 2, Summer 3, Summer 4 [ 193, 196, 197, 198 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9, Summer 2, Summer 3, Summer 4 [ 193, 196, 197, 198 ] Spring 9, Summer 2, Summer 3, Summer 4, Summer 5 [ 193, 196, 197, 198, 199 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Sprint Spring 9, Summer 2, Summer 3, Summer 4, Summer 5 [ 193, 196, 197, 198, 199 ] Spring 9, Summer 2, Summer 3, Summer 4, Summer 6 [ 193, 196, 197, 198, 200 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3790 [ IGBF-3790 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                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 -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                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 ]

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: