Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Spring 4, Spring 5, Spring 6, Spring 7, Spring 8
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.
Attachments
Issue Links
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- To-Do
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Activity
Try to finish draft by the end of March 15th (Thursday)
I brushed up the SRA section and made it cleaner.
Moving ticket to first level review:
- Check for grammar and spelling
- Add comments and ideas for others
- Make sure there is formal writing, no "we's" or "I's"
- Past tense
- Make sure sections flow together and are connected
- See if there is anything else you would like to add to the next draft
Note: This review is for all writers. Once finished reviewing comment that you are finished.
Submit data to IGB Quickload Note: I created a list of tasks to perform for the IGB quick load section of the document but need to confirm with Dr. Loraine that these steps are correct before moving forward.
Thanks Molly Davis and Robert Reid for this!
I have a couple of minor editing requests that I think can be done as part of this first draft.
Kicking it back to "To-Do" for Molly to take a look.
If you address a comment and are pretty confident that your change takes care of it, it's fine to delete or "resolve" the comments. Once you're happy with the edits, please move the ticket all the way to "Needs testing" for one last read-through (by me and/or Robert Reid) and we'll hopefully close it out this first draft!
Thanks Molly Davis for addressing my last batch of comments.
I have some new questions now. Please take a look when you get a chance! Thank you 
!
Also, just to let you know: I've been using the document to run a new set of samples from tardigrade and it's been super helpful. Thank you for making this easy!
One idea related to this.
I am mid editing and reviewing of the document now.
I came across the following site for protocols:
Let's chat whether we want to submit this to such a place?
Here is an example of how we could add our pipeline document to protocols website:
https://www.protocols.io/view/a-bioinformatics-pipeline-for-processing-and-analy-kxygxp77wl8j/v1
I am going to have Brandon the Masters student join me this summer via other funds.
I think it would be a good thing to see if he, with a more limited experience in bioinformatics can walk through this protocol on the cluster.
He will officially start after exams. But I will get him started now getting accustomed to navigating the cluster.
It will be a good way to see where in the doc, we need more clarity!
Rob
Submit data to IGB Quickload:
I wonder if this section should be its own public protocol?
All done with review.
We should gather and chat how we want to proceed, aka protocols.io, etc.....
R
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.
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.
Moving this ticket to done and making a Draft 2 ticket with new requests!
Google Document: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing