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  1. IGB
  2. IGBF-3727

Create new input file for checking SRA code

        Details

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

          Description

          In the code repository there is a file used to compare the results of running the rnaseq pipeline before and after the data were sent to SRA.

          This file is:

          • SRP460750-ARE-timecourse/CheckSRASubmissions/input_data/CheckSRA-SL5.xlsx

          For this task, please create another tab in the file named something different from the existing tabs.

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              relates to

              Task - A task that needs to be done. IGBF-3683 Update SRA to use the correct sample codes for Muday lab time course data

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3720 Re-run Nextflow Muday time course data again with SL5 and data downloaded from SRA

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3683 [ IGBF-3683 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3720 [ IGBF-3720 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Summary Compare Original muday time course data to SRA re-run data Create new input file for checking SRA code
                ann.loraine Ann Loraine made changes -
                Description In the code repository there is a file used to compare the results of running the rnaseq pipeline before and after the data were sent to SRA.

                This file is:

                * SRP460750-ARE-timecourse/CheckSRASubmissions/input_data/CheckSRA-SL5.xlsx

                For this task, please create another tab in the file named something different from the existing tabs.


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                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3727

                Note: Includes a new tab in the CheckSRA excel sheet that has the new general statistics from the multiQC report called 'Updated_SRP460750'

                Show
                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3727 Note : Includes a new tab in the CheckSRA excel sheet that has the new general statistics from the multiQC report called 'Updated_SRP460750'
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis 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 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                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 ] To-Do [ 10305 ]
                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 -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment - - edited

                Reviewing by retrieving the new version of the file and opening it in some new code.

                Note:

                I had to make an edit to CheckSRA.Rmd to enable it to open a file with required input data, the file having changed position in the repository file tree. I haven't pushed that change to the repository yet.

                Show
                ann.loraine Ann Loraine added a comment - - edited Reviewing by retrieving the new version of the file and opening it in some new code. Note: I had to make an edit to CheckSRA.Rmd to enable it to open a file with required input data, the file having changed position in the repository file tree. I haven't pushed that change to the repository yet.
                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
                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 ]
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                ann.loraine Ann Loraine added a comment -

                The data file worked well with the new code. Please submit PR when ready.

                attn: Molly Davis

                Show
                ann.loraine Ann Loraine added a comment - The data file worked well with the new code. Please submit PR when ready. attn: Molly Davis
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/47

                Show
                Mdavis4290 Molly Davis added a comment - PR : https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/47
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis 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 ]
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                ann.loraine Ann Loraine added a comment -

                PR is merged. Since I already tested the new file, I am moving to Done without the extra additional post-merged testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is merged. Since I already tested the new file, I am moving to Done without the extra additional post-merged testing.
                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:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: