drpatelh
commented
2 years ago We need to bring all of this documentation together in a consistent manner on the website. The plan will be to point users to the website if they ask questions of Slack and then to replace existing documentation in the pipeline usage.md with a link to these docs.
Existing documentation
Overwriting resource requests
https://github.com/nf-core/viralrecon/blob/master/docs/usage.md#custom-configuration Should be added https://nf-co.re/usage/configuration#tuning-workflow-resources
Overwriting container definitions
https://github.com/nf-core/viralrecon/blob/master/docs/usage.md#updating-containers Should be added as a new section in https://nf-co.re/usage/configuration
Overwriting non-mandatory parameters via task.ext
https://nfcore.slack.com/archives/C0110R22NH3/p1646299213645449?thread_ts=1621939743.039300&cid=C0110R22NH3 https://github.com/nf-core/rnaseq/issues/756#issuecomment-1039394586
Should be added as a new section in https://nf-co.re/usage/configuration
Using params.yml instead of -c to provide parameters
https://github.com/nf-core/viralrecon/issues/283#issuecomment-1046237471
Should be added as a new section in https://nf-co.re/usage/configuration (at the top: very important to have this visible)
TODO
We need to figure out how we version this documentation in anticipation of big changes in the DSL2 syntax.
cf https://github.com/nf-core/tools/pull/1353#pullrequestreview-831612660