'How to get the path of the current temporary working directory in nextflow
I'm trying to create a file in the processes temporary directory that is checked by nextflow for output using the native scripting language (Groovy) of nextflow.
Here is a minimal example:
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
process test {
echo true
output:
file('createMe')
exec:
path = 'createMe'
println path
output = file(path)
output.append('exemplary file content')
}
workflow {
test()
}
Simply creating the file in the current directory would work when using python as the scripting language, but here it fails with this message:
Error executing process > 'test'
Caused by:
Missing output file(s) `createMe` expected by process `test`
Source block:
path = 'createMe'
println path
output = file(path)
output.append('exemplary file content')
Work dir:
/home/some_user/some_path/work/89/915376cbedb92fac3e0a9b18536809
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
I also tried to set the path to workDir + '/createMe', but the actual working directory seems to be a subdirectory of that path.
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|
