These are chat archives for nextflow-io/nextflow

25th
Nov 2018
Tobias "Tobi" Schraink
@tobsecret
Nov 25 2018 03:51
Is there an environmental variable that can be accessed from inside the pipeline script, that tells me where the script is located? Use case: storing dependencies that I cannot find in conda in the same folder as the pipeline script but do not want to hard code the path but want to use a relative path.
Rad Suchecki
@rsuchecki
Nov 25 2018 05:15
Just place these in bin subdirectory of your pipeline? @tobsecret
Tobias "Tobi" Schraink
@tobsecret
Nov 25 2018 05:35
oh, that works?
I'll try that!
Thanks!
Paolo Di Tommaso
@pditommaso
Nov 25 2018 08:26
option 2. use baseDir implicit variable, see here
Maciej Pawlaczyk
@Fizol
Nov 25 2018 11:24
What's baseDir in that case, from where it comes from?
If I have some scripts I can't install on the path or copy to bin I wrap my nextflow script with additional env variables.
Tobias "Tobi" Schraink
@tobsecret
Nov 25 2018 14:16
Thanks folks!
Paolo Di Tommaso
@pditommaso
Nov 25 2018 17:20
What's baseDir in that case, from where it comes from?
it's an implicit variable representing the directory where the main script is located
tbugfinder
@tbugfinder
Nov 25 2018 17:23
In which folder so you usually execute nextflow and keep the logs?
Paolo Di Tommaso
@pditommaso
Nov 25 2018 17:25
it depends, when deploying a workflow hosted on GitHub that baseDir is basically the path where the repo is cloned which is different from the launch dir
Paolo Di Tommaso
@pditommaso
Nov 25 2018 17:55
cast your vote