h3abionet / h3abionet-sops Goto Github PK

At the SAB meeting discussion arose about possibly using this repo for all H3ABioNet SOPs, not just those for workflows. If so, we will need to think about how to reorganize this appropriately to account for SOPs from other projects, such as FAIR, training, RedCap, etc.

This is a general ticket for tracking 16S updates based on the discussions held at the AGM meeting on 2021-08-30. A few items were noted, in particular:

1. possibly have the 16S SOP possibly hew closer to the training materials used with the IBT course
2. have accredited nodes review and recommend edits to the current SOP based on their experiences with the accreditation exercise.

We are updating the RNA-SOP to include:

• Reproducible Research description

• Update references and format appropriately

Work will be done on the jdrnevich-RNAseqUpdates branch

Action items from September meeting:

• Create technical documentation (or how-to guide) for adding new SOPs
• Add suggestions for effective SOP writing (sections, style, references, .. etc)

A few features to consider in the final site:

• Reachability/ navigation: from any point in the site to any other (whether on the page itself or on other pages)
• Proper credit to SOP authors
• Help text for common abbreviations/ keywords
• Social sharing
• Ability to comment and discuss by the community (not necessarily through Github issues)
• Maintainability

Originally posted by @azzaea in #5 (comment) and @lsmainzer in #5 (comment)

A few updates for the SOP:

• Add Best Practices reference (and possibly Fig1)
• Require both methods for the exercise
• Update intro section to emphasize building up knowledge and background prior (lit review).

Per Slack w/ Faisal:

cjfields [10:07 AM]
Ok
One other point that might be worth thinking about. We have two alternative methods (alignment and pseudoalignment); should they know both or only be required to run one? It's not clear in the SOP.
Some of the questions expect both. Most obvious: "How do counts between the two methods (alignment vs. pseudoalignment) compare?"

Faisal Fadlelmola [10:08 AM]
I think it better to include both

cjfields [10:09 AM]
I agree
I can tweak the wording with that in mind

Faisal Fadlelmola [10:10 AM]
A survey of best practices for RNA-seq data analysis
this is one of the best paper we used during our assessment

cjfields [10:11 AM]
Is that referenced in the SOP?

Faisal Fadlelmola [10:11 AM]
no

cjfields [10:11 AM]
We can easily add it
I'm going to add a Github issue to track these two points (requiring both methods, adding the reference) to make sure they get done
Just in case

Faisal Fadlelmola [10:13 AM]
I like their Figure 1:
Pasted image at 2018-10-30, 6:12 PM

cjfields [10:14 AM]
Can see if that's Creative Commons, if so we could add it in as well.

Faisal Fadlelmola [10:15 AM]
Citation: A survey of best practices for RNA-seq data analysis

Genome Biology, 2016, Volume 17, Number 1, Page 1
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi

I noticed a number of the practice data set links are broken, likely from old URLs. Examples:

Variant calling: http://h3data.cbio.uct.ac.za/assessments/NextGenVariantCalling/practice/
16S: http://h3data.cbio.uct.ac.za/assessments/16SrRNADiversityAnalysis/practice

The master branch is based on the Cayman theme, which is really nice. However, for the longer SOPs, navigation and scrolling down the page becomes somewhat cumbersome. Alternative views are implemented in the other 2 branches:

• The tst_cayman_sidebar uses the same cayman theme as master, but adds a few buttons at the top for easier navigation (instead of the download links), and there is also a side bar hosting the table of contents for the given page.
• The tst_minimal_mistakes has better control abilities for the location of the table of contents, and its also easier to link to the page's authors (as in the RNA Seq SOP for example).

We need to move this repo under the H3ABionet Github group

This is not an issue per say, but a useful hint I guess, following some discussions with @ameintjes.

This is a handy script for converting a docx file into markdown. It only requires pandoc to be installed in your system (version 1.18 works for me, but with older versions, I had problems with pictures). Code credit goes entirely to Jesper Rønn-Jensen entries here. Images would be nicely extracted, but tables might require more manual intervention.

This is now in place under pages/misc/; the text is a direct conversion of the original 'Reviewer Overview' draft. This will need to be modified for addition to the main site.

We need a DOI associated with this repo.