Open ewels opened 7 years ago
Oops, this got a bit longer than I intended.. But each bit doesn't need to be very long. Maybe different markdown files with each of these as a header? Then copy in a short code example if it's not very long.
Phil
I've tried starting on this several times now but I struggle to get anywhere since a lot of this seems redundant. Most points are covered pretty well by the official Nextflow documentation, example scripts or FAQ. I agreed that it would be nice to show how we tend to write scripts (with separate config files etc.) but a more generic help documentation seems a bit out of our scope.
Pipeline Scripts
tag
)params
(mention need for explicit defaults)FromFilePairs
) and single-end (FromPath
)cpus
,memory
,time
etc)errorStrategy
,maxRetries
etc)publishDir
, different modes, usingparams.outdir
)bin
directory for bundling scriptsConfig files
Running on UPPMAX
params.project
,params.clusteroptions
)process.queue = 'devcore'
)params.genome
, creating channels from paths, using these channels in a way that they are not consumed)Running outside UPPMAX
Bonus features
main.nf
etc)NGI-xyz
, readme template, versioning)Common Processes
params
and grouped presets)