A community effort to collect a curated set of analysis pipelines built using Nextflow.

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&gt; Hi Kairi, as far as I know you could either point to a single directory where the singularity cache would be stored (in your config(s)) and that could be reused throughout your runs and/or cleaning the cache directly in the `.singularity` directory which will force the image to be pulled again 

Simply removing the dirs/files would clean the cache (there should also be a dedicated singularity command to that) and the `cacheDir` directive in the singularity could be used like this
```singularity {
    cacheDir = 'path/to/dir'
}```

Hope that helps ! :slightly_smiling_face:

I was also curious to see if there are ways I can specify parameters per tool?

for example if I want isofox to be a bit more lenient with min_fragment_support or other parameters would there be a way to specify this?

Yes! You could do this with your config file using the process scope and select them by name (`withName`) and adjust the flags of interest :) 

Thanks for the quick response!
I had looked through the FAQ previously, which was extremely helpful. However, I was wondering if there was a way to see all the available flags that I could customize?

Please let me know if I am missing something. Thanks so much!

My pleasure! For that you can check out the WiGiTS repo directly for the process/module-level flags and detailed explanations of the tools themselves :) <https://github.com/hartwigmedical/hmftools|https://github.com/hartwigmedical/hmftools>

Hey!
I was also wondering for WES I'm assuming I have to run in targeted mode. If this is the case I should be providing a bed file as well as generating my own panel correct?

Yes, you need to use the panel resource creation workflow that you can find on the WiGiTS repo - it’ll be part of oncoanalyser in the next release ! :) 

So if this is the case I currently cannot generate these panels on oncoanalyzer correct?
I'm assuming I need to copy the repo in order to generate these panels?

Not yet no, you could try to use the dev-2.2.0 branch of the repo but that's still in development - otherwise yes, the hmftools repo would be the place to start