j35p312 / fluffy Goto Github PK

There has been some issues lately where samplesheets are getting updated in workflows, hindering smooth processing done by fluffy. I believe that fluffy should be turned into a tool where it only handles the analysis of data. That way, a monolithic solution such as cg can handle all the pre-analytical parts of this tool - thus letting fluffy do what fluffy does best - analyse the data.

I want to know how we can use fluffy? It has wisecondorX, PREFACE and AMYCNE joined in it. How it can tell about fetal gender and fetal fraction?

The scripts in: fluffy/fluffy/scripts/ are executed in a sbatch scripts. However they do not activate any environment, but rather use the python binary that happens to be available, this is an unexpected behavior that makes the pipeline crash unless the "correct" python version and dependencies happens to be available.

For instance like this:

Traceback (most recent call last):
  File "/home/proj/production/bin/miniconda3/envs/P_fluffy/lib/python3.7/site-packages/fluffy/scripts/generate_csv.py", line 7, in <module>
    import numpy
ModuleNotFoundError: No module named 'numpy'

Would is be possible to include these scripts in a singularity image or the main Fluffy installation?

Hello
blacklist bed file, is it generated with WisecondorX for each sample or referrent?