Add prefix to counts matrix and MultiQC so they won't all have the same name

[PhilPalmer]

Problem

All of the CSV counts matricies and MultiQC HTML files have the same name which can make comparing these files between different runs more difficult

Solution

Add a prefix to these files that is defined by the user a parameter and can be unique to each run

Implementation

• Add a new run_name parameter (see How can I additional parameters to the Nextflow script? #123 for how to add new parameters)
• Change the MultiQC output name here
  • Update the output for the MultiQC process here to reflect any changes in the multiqc report filename(s)

Note: it may be best to make a copy of the multiqc_report.html here because CloudOS requires it to have this specific name in order to render it directly on the platform

[lmurba]

@PhilPalmer do you want me to take care of this issue? Or are you working on it?

[PhilPalmer]

Yeah, it's great if you're able to take of the issue! I feel like there's no stopping you getting through all of these issues which is awesome 😂

The work in progress was just because I hadn't finished the implementation section of this issue. I've just finished doing that now. A couple notes on that:

1. I can rebuild and push the Docker container once you have updated the post-processing script
2. It may be best to make a copy of the multiqc report rather than changing it's name (see comment from above)

Note: it may be best to make a copy of the multiqc_report.html here because CloudOS requires it to have this specific name in order to render it directly on the platform

[lmurba]

@PhilPalmer You've taught me so much so now I feel like I can actually do stuff! I'm really excited about that haha

Ok yeah that makes sense. I'll reach out if I have any questions or issues and I'll show you want I did when I'm done before I merge.

Thanks!

[PhilPalmer]

Haha, that's great to hear, thank you! I feel like you've taught yourself a lot as well

A couple more things I just thought of:

1. What do you think would make sense for the default value or behaviour for this run name parameter?
2. A more general comment is that you could download and use VS Code (or another IDE) to write/develop code even if you're only testing on Sumner. You don't necessarily need Nextflow on your laptop

[lmurba]

@PhilPalmer

1. What if we automatically added the date as a prefix and had the option to add a run name. So default would be just the date? Is this doable? @angarb What are your thoughts?

2. I will do that!

[PhilPalmer]

If you want the date as a prefix you could use something like, workflow.nextflow.timestamp. The value of this would be in the following format for example, so may need a tiny bit of reformatting:

22-01-2019 11:19 UTC

The default could also be no run_name as long as you appropriately deal with this scenario

[lmurba]

Ok I think I have an idea. I'll show you when I'm ready and you can see what you think.

[lmurba]

@PhilPalmer, @angarb and I decided we don't want to change any of the prefixes for rmats (we think these are fine as is). With that being said, I'm going to remove those tasks from the implementation, ok? I've added the prefix for the counts already now I just need to update the MulitQC. Any recommendation on how to move the files and then rename them?

[lmurba]

fixed here