millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-20 23:32:05 +00:00
Code Issues Releases Packages Activity

test: Use profile ENV variable hack

Browse source 
The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
This commit is contained in:
Edmund Miller 2021-02-02 11:55:41 -06:00
parent e7b1241449
commit ddbca7b467
No known key found for this signature in database
GPG key ID: BD387FF7BC10AA9D
1 changed files with 8 additions and 13 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

21
tests/config/nextflow.config
View file

@ -1,20 +1,15 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
if("$PROFILE" == "docker") {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
} else if ("$PROFILE" == "singularity") {
singularity.enabled = true
singularity.autoMounts = true
} else if ("$PROFILE" == "conda") {
params.enable_conda = true
}