Facilitator training content feedback

[rsuchecki]

Handout version

1a07f4e

Action points

• introduce -resume early and use unless explicitly not needed
• drop NF Git integration, consistently use git directly
• Consider re-creating Figure 4 (Nextflow building blocks). Currently each output is depicted as separate - which is correct but the concept of input and output channels for a process could be better explained if outputs of all tasks end-up in a channel.
• Additional/extended info/note box indicating alternative ways in which script can be included in a process (different string delimiters, !{shell} syntax, bin, templates).
• Show the data after setup_data.nf exec. Both as instruction and (partial) output in handout. no longer needed as local dat aused
• More generally, add ls, tree and less somefile more often in instruction to encourage participants to stop and think before pasting another command block.
• In failed job question explicitly ask about the Command error: output block as there are many other bits of info on screen.
• Consider moving not-covered parts of nextflow.config to other, included config file(s)
• Consider further simplifying the workflow.
• Singularity pull may fail - a re-run is sufficient, but a local copy of the image should be provided with path to be passed at run time param if needed

Example workflow

• Convert bash to NF live code input processing and one or two processes
• Participants to implement another two or three processes

Trainee tasks

• Break-up ternary in .take() condition into more reader friendly syntax, note that -1 means take all.
• Make channel names in .into{} more explicit e.g. readPairsForTrimmomaticChannel
• Provide more info on non-NF content e.g. samtools merge syntax
• More info on syntax, e.g. use of quotes when e.g. process.executor = 'slurm'
• Should the channel consumed by bam_merge be declared upstream or should that be the first part of the task?
• More links to appropriate sections of the documentation
• Be generally more precise and explicit about the tasks - leave less to interpretation

Slides

• Detailed, step-by-step explanation of process definition