Add information about how to use ext in a custom config file

[maxulysse]

cf https://github.com/nf-core/tools/pull/1353#pullrequestreview-831612660

[drpatelh]

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.