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Allow to use environment variables at parameters
Description
Current implementation only allows to use baseDir
, projectDir
, launchDir
and secrets
at the parameters file or from the command line.
This pull request adds also the option to access the environment variable available at config scope. They can be referenced using the prefix env.
, like ${env.MY_ENV_VAR}
.
Usage
Example on how to use it:
$ cat ../params.yml
outdir: ${env.NXF_WORK}/results_workdir
$ ./launch.sh run nextflow-io/rnatoy -params-file ~/tmp/params.yml -e.NXF_WORK=/home/jordeu/tmp/nextflow -with-docker