Parsing from initial run argument into process scripts
DolapoA opened this issue · 3 comments
DolapoA commented
How do I parse an argument from the initiation command into one of my process scripts that's in another language like Python.
Initiation cmd:
nextflow run /Path/to/myscript.nf --in '/Path/to/MyData'
process dataDirectories {
"""
#!/usr/bin/env python2.7
import os
import getpass
currentUser=getpass.getuser()
dataPath="/home/" + currentUser + "/WGS_Data/" + MyData
resultsPath="/home/" + currentUser + "/WGS_Results/" + MyData
try:
os.makedirs(dataPath, 0o777)
os.makedirs(resultsPath, 0o777)
except:
pass
"""
}
I would like to get the string 'MyData' from the path (which is in my '--in' argument) into my python script.
Can this be done?
pditommaso commented
It's just a matter of string interpolation e.g. "/WGS_Data/${params.in}"
DolapoA commented
Ah yes that works thanks bro.
pditommaso commented
Enjoy