nf-core
`nf-core subworkflows test` `--profile` flag doesn't like specifying `docker` or `conda`
Description of the bug
$ nf-core subworkflows test --profile docker
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13.1 - https://nf-co.re/
Usage: nf-core subworkflows test [OPTIONS] subworkflow name
Try 'nf-core subworkflows test -h' for help
╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮
│ Invalid value for '--profile': 'docker' is not one of 'none', 'singularity'. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
[10:43](https://nfcore.slack.com/archives/D017F3SUESW/p1713429815891469)
$ nf-core modules test --profile docker
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13.1 - https://nf-co.re/
WARNING 'repository_type' not defined in .nf-core.yml
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» Pipeline
nf-core/modules
### Command used and terminal output
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### System information
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hey, I also tried the gitpod devcontainer for the raredisease pipeline and had some weird issues with running docker - the docker daemon was not running upon container start and needed to be started manually, then permission issues prevented us from running docker without sudo and when we run nextflow it doesn't allow us to use sudo. It would be nice to solve these issues. What is the intended use of the gitpod container, should the user gitpod be able to run stuff directly? Is the conda environment supposed to be turned on always?
adding the gitpod user to the docker group seems to fix the permissions issue when using docker: usermod -aG docker gitpod. Starting the docker daemon could be done in a post-build script when spinning up the container.
