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test: Use profile ENV variable hack

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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
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GPG key ID: BD387FF7BC10AA9D
1 changed files with 8 additions and 13 deletions
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13
tests/config/nextflow.config
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@ -1,20 +1,15 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
if("$PROFILE" == "docker") {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
} else if ("$PROFILE" == "singularity") {
singularity.enabled = true
singularity.autoMounts = true
}
} else if ("$PROFILE" == "conda") {
params.enable_conda = true
}