Items for review / fixing / todo

[PaulHancock]

• [x] check out options for using {: .language-groovy} to format nextflow things
• [x] Front pages AEST -> AEDST
• [x] Add intro page
  • [x] Acknowledgement of country (Curtin + UWS)
  • [x] Icebreaker - describe a workflow that you'd like to automate
  • [x] Include etherpad details
  • [x] links back to training site
  • [x] link to teams meeting
  • [x] Add link to teams meeting
• [x] Workflows and Pipelines
  • [x] research example -> make numbered list
  • [x] add keypoints
  • [x] exercises (all) ask people to share in etherpad
  • [x] forward/backward note:
  • [x] change to input/output driven descriptions
  • [x] make a note about caching of already completed work
• [x] Intro to nextflow
  • [x] Remove new line in first quote.
  • [x] rename documentation -> where to get help
  • [x] make note about clearing output for the nextflow console
  • [x] channel section
  • [x] invite users to play along using the console
  • [x] provide some dummy files for people to use (bigfile.txt eg)
  • [x] check the '/data/big/' -> '/data/sum'
  • [x] process
  • [x] note the difference between shell and script, remove 'exec' so people don't ask questions
  • [x] note that 'script' is the default behaviour
• [x] Nextflow Workflows
  • [x] worflow -> workflow
  • [x] variables (update name to plural)
  • [x] add note about shell/exec and the !/$ variable
  • [x] note about variables being defined as params.variable and then called as ${variable}
  • [x] note about where the 'message.txt' file is being stored (work/etc/etc/)
  • [x] Why do we want to manipulate channels -> all about channels and why we manipulate them
  • [x] Begin within motivation as to how channels are the very important, and manipulating them is very powerful. Simple processes, driven by complex channels.
  • [x] add more dummy files for the examples here, update the outputs.
  • [x] add files to a 'data' or 'examples' directory (and as a .tar file) for people to download
  • [x] channel manipulation example
  • [x] add comments to note the output for each of the processes (eg dimension of lists etc)
  • [x] remove .collect() or make a comment that it is redundant
  • [x] groupTuple
  • [x] Shorten path name in output to be more clear
  • [x] example -> put the '.' at the start of the new line
  • [x] cross example -> add .basename so this will work on files rather than strings.
  • [x] expand on the publishDir description
• [x] Orchestration
  • [x] move section "labels" to be after the singularity section
  • [x] make a challenge in two parts
  • [x] use different containers for different jobs (maybe look for some small containers for an example) eg, matplotlib and tensorflow containers
  • [x] get people to submit different labelled jobs to different job queues with different mem/cpu requirements
• [x] Containers: Swap to be before Orchestration
  • [x] Listing and viewing /deleting docker containers with docker ps etc

[PaulHancock]

• [x] Update schedule to include breaks
• [x] Update schedule on front page (html) and WelcomeIntro (md)
• [x] Add link to WelcomeIntro to the main page (in the schedule?)