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  1. IGB
  2. IGBF-3622

Create a Draft 1 Pipeline Document

        Details

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

          Now that we have used the pipeline multiple times successfully, it is time to write a paper about every step in detail. This is to ensure that methods are documented and not forgotten. The pipeline would include submitting data to SRA, using the data from SRA, running the data through nextflow nfcore, sanity check the data with original data, submit data to IGB quick load.

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              relates to

              Task - A task that needs to be done. IGBF-3709 Edit Draft 2 of the pipeline document

              • Major - Major loss of function.
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                Mdavis4290 Molly Davis added a comment -

                Moving this ticket to done and making a Draft 2 ticket with new requests!

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                Mdavis4290 Molly Davis added a comment - Moving this ticket to done and making a Draft 2 ticket with new requests!
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                ann.loraine Ann Loraine added a comment -

                A request for Molly Davis:

                Could you take a look at the new comments I added regarding the "prefetch" code? It looks to me like the script can only work if the user doesn't try to run an interactive session.

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                ann.loraine Ann Loraine added a comment - A request for Molly Davis : Could you take a look at the new comments I added regarding the "prefetch" code? It looks to me like the script can only work if the user doesn't try to run an interactive session.
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                Mdavis4290 Molly Davis added a comment -

                Format the draft in another document that would work with protocols. Use the protocols example above to understand formatting. Then move this ticket to testing for Brandon to test Draft 1 pipeline document.

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                Mdavis4290 Molly Davis added a comment - Format the draft in another document that would work with protocols. Use the protocols example above to understand formatting. Then move this ticket to testing for Brandon to test Draft 1 pipeline document.
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                robofjoy Robert Reid added a comment -

                All done with review.
                We should gather and chat how we want to proceed, aka protocols.io, etc.....

                R

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                robofjoy Robert Reid added a comment - All done with review. We should gather and chat how we want to proceed, aka protocols.io, etc..... R
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                robofjoy Robert Reid added a comment -

                Submit data to IGB Quickload:

                I wonder if this section should be its own public protocol?

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                robofjoy Robert Reid added a comment - Submit data to IGB Quickload: I wonder if this section should be its own public protocol?
                8 older comments

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    • Created:
                      Updated:
                      Resolved: