lizzyparkerpannell / untargeted_metabolomics_workflow Goto Github PK

• all functions into 00_functions_whole_workflow or similar
• clean functions out of script for each stage
• add source code for 00_functions_whole_workflow at start of each stage script

Have added flavicon.png to static/images but isn't working yet.

Search within code to find how to change RSE flavicon to untargeted-metabolomics-workflow flavicon

We already have a glossary in the drive - bring this across to website and add references

• add folder called glossary
• add index.en.md file to that folder
• populate it with glossary in md
• check links and weighting on website

Heather has a paper with the in house prefered plant extraction protocol.

Overy SA, Walker HJ, Malone S, Howard TP, Baxter CJ, Sweetlove LJ, Hill SA, Quick WP. Application of metabolite profiling to the identification of traits in a population of tomato introgression lines. J Exp Bot. 2005 Jan;56(410):287-96. doi: 10.1093/jxb/eri070. Epub 2004 Dec 13. PMID: 15596481.

Either as a paper of as a bullet point extractions doc

This should list 8, only list one when I run it in R
source("https://raw.githubusercontent.com/LizzyParkerPannell/Untargeted_metabolomics_workflow/main/00_workflow_functions.R")

Need to fill in the content text for each stage of the workflow. This will need some adjustment to make it more appicable to those outwith UoS.

Update <index.en.md> in each of these folders

• 01_
• 02_
• 03_
• 04_
• 05_
• 06_
• 07_

• Use mermaid to recreate workflow diagram
• Add links (shortcuts) within workflow diagram
• embed mermaid diagram on website 00_Overview/05_workflow_diagram.en.md

• James: you can add your issues (as separate issues or check boxes in a list within one issue)

Find a fix for the netlify link

Hi Lizzy,
I think there is an issue with people understanding the file locations and where to be working from in steps 4 and 5. I keep on getting questions about why code isn't working for them and it is usually because they've got too many subfolders, or the samplelist.csv or treatments.csv in the wrong place.
It would probably clear things up to have a screen grabbed example of the lay out of the files. Showing the root folder, the mass up output folders and their contents, and where the metadata files should go.
I would do this but have no mass UP processed files, and in all honesty am not 100% sure myself.
Hope that makes sense
James

From Rachel : "it can't load Muma package, it seems to have been archived in May. I've selected older versions of R in RStudio but the rest of the packages need the most updated version of R."

Add the following to the index of each chapter, with the title altered

---
chapter: true
date: "2022-11-08T11:19:11+01:00"
pre: <b>00. </b>
title: Overview of workflow
weight: 1
---

• 01_
• 02_
• 03_
• 04_
• 05_
• 06_
• 07_
• 08_

• add static folder
• add static/css folder
• have a go at adding code from https://github.com/RSE-Sheffield/git-github-zero-to-hero/blob/master/static/css/theme-rse-learn.css to static/css
• ... and adding code from pygments.css
• add config files to root folder

• When the preprint is published, link to DOI
• When manuscript is published link to DOI in repository

• find a way to upload .mzML (currently too big for github!) link to external hosting?
• upload .mzML converted files and treatments.csv and samplelist.csv
• upload peak table created with MassUp
• create demo data README.txt including link to paper and thesis and citation info

• info on different types of MS for untargeted analyses
• highlight ones we cover in this workflow
• brief pros/ cons of ones we cover in this workflow
• useful reviews/ refs for decision making
• link to workflow diagram and explain that type of (LC)MS affects how you process the data

• landing page title
• title for each chapter within _index.en.md

• lkshf

• create an archetypes folder
• create archetypes/chapter.md file and fill with:

+++
title = "{{ replace .Name "-" " " | title }}"
date = {{ .Date }}
weight = 5
chapter = true
pre = "<b>X. </b>"
+++


# Some Chapter title

Lorem Ipsum.

• create archetypes/default.md file and fill with:

+++
title = "{{ replace .Name "-" " " | title }}"
date =  {{ .Date }}
weight = 5
+++

Lorem Ipsum.

• convert stages to custom numbered list (stages of the workflow)
• remove duplicated title (stages of the workflow)
• convert list of example file names to secondary indented bullet list (assumptions)
• remove duplicated title (assumptions)
• remove duplicated title (experimental structure)
• remove duplicated title (workflow diagram)

Especially the MALDI-quant parts

• Alter all cases of index.en.md to _index.en.md --> this is why menu wasn't working!!!

Set up folder structure for a website to document the workflow

• create content folder
• create folders for each stage of the workflow within content e.g. 00_overview
• create folders called faq_glossary_links and setup
• create files called index.en.md, credits.en.md and snippets.en.md
• within each subfolder, create index.en.md with title of section

Now that we've sorted the file conversion parameters to get MALDIquant to work in R, can adapt the workflow with MassUp being optional (still good for QC)

• update R codes for step 04_data-preprocessing (MALDI and DIMS)
• update guide/ documentation to explain the options
• link directly to MALDIquantForeign and MALDIquant vignettes as these are very good