nextflow run in docker with conda environment

[COMODr]

When I run a work flow with nextflow in a docker image, it can excute successefully. But when I run nextflow script with '-with-docker [docker image]', it will get an error "Conda prefix path does not exist or it's not a directory". How can I sove this problem.

[pditommaso]

This looks a problem in the configuration. please provide e a replicate test case

[COMODr]

Like this attachment example 1、docker run -it test.nf It can execute successfully 2、nextflow run test.nf -with-docker rnaseq:v1.5.3 conda environment is in the docker image, the 2d sctript will get this error "Conda prefix path does not exist or it's not a directory" Thank you very much for your reply and look forward to your help. At 2021-12-20 17:10:37, "Paolo Di Tommaso" ***@***.***> wrote: This looks a problem in the configuration. please provide e a replicate test case — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.Message ID: ***@***.***>

[pditommaso]

This is a pipeline specific problem, not a NF issue. You should consider reporting it to the corresponding project repo https://github.com/nf-core/rnaseq/

[COMODr]

This example is just something I created by myself. The cause of this problem seems to be the "nextflow run <nfwork> -with-docker rnaseq:v1.5.3" can't map the conda environment path in the script to the Docker container. Whether it is that conda environment cannot be used in a scripts when executing with Docker containers. Although the problem was not solved, thank you for your reply in your busy schedule. At 2021-12-20 19:38:58, "Paolo Di Tommaso" ***@***.***> wrote: This is a pipeline specific problem, not a NF issue. You should consider reporting it to the corresponding project repo https://github.com/nf-core/rnaseq/ — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.Message ID: ***@***.***>