Make --outdir a mandatory parameter

[drpatelh]

Description of feature

We need to re-assess what we set --outdir by default in the nf-core pipeline template.

It is currently set to ./results which is fine for shared file systems / HPC environments but with the growing adoption of Cloud this simply doesn't work anymore and can end up costing money and time if an absolute path isn't provided instead of a relative one. e.g. on AWS Batch, by default the results will get written to the head node and are lost with it.

We have tried to add a solution that checks if we are using -profile awsbatch and to raise an error if we aren't using an absolute path here but that will only work for those using -profile awsbatch and so isn't a generic solution.

The only solution I can see is to make --outdir a mandatory parameter. This would avoid silent failures at the very least and can easily be set to the current default value within a config albeit a local or institutional one.

[drpatelh]

One problem we have here is that if we set --outdir = null in nextflow.config then tracedir gets evaluated to null/pipeline_info even if --outdir ./results is specified on the CLI.

Wondering what the best solution is here 🤔 Ping @mahesh-panchal

CORRECTION: All is good here! I just realised that the reason I get an output dir called null is if you don't specify --outdir - in this case a schema validation error is generated asking you to use it. On adding it to the CLI then the trace files are published in ${params.outdir}/pipeline_info as expected.

As you were.

[pditommaso]

I think it would make more sense to address this on nextflow. Likely adding a configuration setting that when enable instructs Nextflow to resolve relative paths against the work-dir instead of the launching directory. We had already a chat with @jordeu at this regard. Could be an issue opened in the Nextflow repo?

[drpatelh]

Thanks @pditommaso ! Done nextflow-io/nextflow#2661

[drpatelh]

Will be fixed in #1431