error with "nextflow run main.nf -profile standard,test"

[genmaibutter]

I'm a beginner in nextflow pipeline. I have problem with the Execution on a server. I install nextflow with conda by "conda install -c bioconda nextflow" And, I download the StellarPGx by type "git clone https://github.com/SBIMB/StellarPGx.git && cd StellarPGx"

The working directory is in the StellarPGx folder

I type "nextflow run main.nf -profile standard,test" and Enter. Then, I got an error.

Can you give me suggestion.

[twesigomwedavid]

Hi @genmaibutter, Are you using Docker or Singularity on your machine?

Thanks

[genmaibutter]

Sorry for late reply. I try to figure out the system. I have singularity on my machine. Here is happen when I type "singularity" and Enter. Please give me some suggestion. Thanks.

[twesigomwedavid]

@genmaibutter, we are looking into this and will get back to you asap.

I wonder whether the installation of Nextflow using conda is causing the issue since you'd have to be in the right conda environment to run it.

Perhaps try using the nextflow installation via curl -s https://get.nextflow.io | bash Note that this will create an executable nextflow file in your current working directory.

[twesigomwedavid]

@genmaibutter, It seems what was causing this issue was an incorrect/corrupted test file. May you try the current StellarPGx code to see if the issue is resolved on your end?

in order not to lose any local changes you can do:

git stash
git pull
git stash pop