Help running test profile

[telatin]

Hello there!
I tried the pipeline as:

nextflow run hoelzer-lab/rnaflow -profile test,local,docker

N E X T F L O W  ~  version 21.10.6
Pulling hoelzer-lab/rnaflow ...
 downloaded from https://github.com/hoelzer-lab/rnaflow.git
Launching `hoelzer-lab/rnaflow` [angry_kalman] - revision: 630e02ef78 [master]
ERROR: Parameter(s) [params] is/are not valid in the pipeline!

and

$ nextflow run hoelzer-lab/rnaflow --help

N E X T F L O W  ~  version 21.10.6
Launching `hoelzer-lab/rnaflow` [silly_mclean] - revision: 630e02ef78 [master]
ERROR: Parameter(s) [params] is/are not valid in the pipeline!

I see nextflowVersion = '>=21.05.0' in the configuration file, and trying with 21.07 or 21.10 things do not improve.

I expect the test profile feeds the corrects parameters to the pipeline so I'm unsure what to do to try running it. I tried with -r 1.4.1 to stick to the last release as well.

Thanks for you help!

[hoelzer]

Hey @telatin ! Thanks for your interest in the pipeline!

That's odd. Your commands look fine. Did you do a nextflow pull hoelzer-lab/rnaflow before? Maybe do it again but I guess that will not change anything.

Another thing is: installing an even newer nextflow version (>23.x.x), which you could also test in a separate Conda environment:

conda create -n nextflow-test -c bioconda nextflow
conda activate nextflow-test
nextflow run ...

I will also try to reproduce your problem when back at some laptop.

[hoelzer]

I just tried it with

N E X T F L O W  ~  version 23.04.1

and

nextflow run hoelzer-lab/rnaflow -r 1.4.1 --help

and it works for me.

I also installed an older version of nextflow via conda:

nextflow -version

      N E X T F L O W
      version 21.10.6 build 5660

and this also worked.

Where do you try to run it? Linux? Laptop or Cluster?

Can you run any other nextflow pipeline?

[telatin]

I was using a cloud VM with Ubuntu, will try again :)
Yes, I can run other pipelines, e.g. nf-core

[hoelzer]

Ok, I am not experienced running nextflow in cloud VMs - yes, please give it another try and let us know if we can be of any further help.