Could not find workflow.nf in the repo.

[ravinpoudel]

I am running steps as suggested in https://github.com/CAMI-challenge/CAMISIM/wiki/User-manual. I could not find workflow.nf script in the repo. Wondering if I am getting the right version of the code/repo?

[AlphaSquad]

Hi, the tutorial for the current version of CAMISIM can be found when clicking on CAMISIM 1.3. There is a new nextflow-based version of CAMISIM in the making and we already updated the wiki accordingly, the nextflow version can only be found on the dev branch. Feel free to already test that, you will have to do a git checkout dev first though.
If you want to use the current/published version of CAMISIM, you should refer to the wiki I linked above. Sorry for the confusion.

[ravinpoudel]

@AlphaSquad Is it possible to provide the conda env yml file that has been tested in the unix env?

[AlphaSquad]

The nextflow version is not extensively tested and there is no yaml file available at this moment

[ravinpoudel]

@AlphaSquad I am trying to run the version that you have suggested above. Installing the required tools in unix is kind a challenge. Wondering if you could share the conda env yml file so that I can create the exact conda env in my machince. I am running in unix system.

[AlphaSquad]

This is an environment with which CAMISIM works on our servers (txt since you cannot upload yml files to issues): camisim.txt. I cannot guarantee this is the minimal set of software required.