Move all the ankflag module within the flagging/ directory of the repo
Remove any need to track the "ankdir"
No need to set ANKDIR environment variable
No need to set params.ankdir in nextflow
No need to hardcode ankdir in python scripts
Remove the need to add an absolute path to the pythonpath
Cause the imports of convertfits and inputs to be relative imports
Use subprocess.run instead of os.system and exit when the sub-command exits
Not done but noted for future use:
from convertfits import *
from inputs import *
Consider avoiding the import * pattern. Instead import what you need explicitly, or use import convertfits as cf and import inputs to keep the namespace clean.
doflag.py could be removed and replaced with bash commands in a Nextflow process
Addressing #480:
ankflagmodule within theflagging/directory of the repoparams.ankdirin nextflowankdirin python scriptsconvertfitsandinputsto be relative importssubprocess.runinstead ofos.systemand exit when the sub-command exitsNot done but noted for future use:
from convertfits import *from inputs import *import *pattern. Instead import what you need explicitly, or useimport convertfits as cfandimport inputsto keep the namespace clean.doflag.pycould be removed and replaced with bash commands in a Nextflow process