add thread/cpu as arg in ds-cgpwgs.pl (ds-wrapper.pl)

[keiranmraine]

Make more obvious how to use rather than just the CPU env variable.

[jsmedmar]

Wondering if OUTPUT_DIR should also be an option?

[jsmedmar]

Nevermind, using HOME should be enough

[keiranmraine]

Both are already added to the in development branch: https://github.com/cancerit/dockstore-cgpwgs/blob/feature/fragmentReadQc/scripts/ds-cgpwgs.pl#L37-L38

[leiendeckerlu]

Hi there,

I think it is the best to reopen this issue here for my question:

I was wondering how to tell ds-wrapper.pl the number of available cores in our system?

I'm using cgpwgs with singularity on our HPC system. In the cwl config file I found this part and I'm now wondering how I can directly tell the wrapper script to use those settings?

hints:

• class: ResourceRequirement
  coresMin: 1 # works but long, 24 recommended
  ramMin: 32000
  outdirMin: 20000

Many thanks!
Lukas

[keiranmraine]

The release has been delayed slightly due to some upstream issues, the option will be released very soon and you can see it here:

https://github.com/cancerit/dockstore-cgpwgs/blob/feature/fragmentReadQc/scripts/ds-cgpwgs.pl#L289

[keiranmraine]

Done