Stack Overflow
Stack Overflow

Questions tagged [ruffus]

Ruffus is a Computation Pipeline library for python.

Ruffus is a Computation Pipeline library for python. http://ruffus.readthedocs.io/en/latest/

7 questions
3
votes
0 answers

Python makefile pipeline using Ruffus

I am trying to pipeline multiple scripts with python framework using Ruffus. I have multiple .cpp and .h files being called from my main.cpp file. My makefile runs perfectly well in shell. How can make a python based pipeline using Ruffus which…
N1P689
  • 45
  • 6
2
votes
2 answers

Can Pweave play nice with Ruffus?

I am interested in developing self-documenting pipelines. Can I wrap Ruffus tasks in Pweave chunks? Pweave and Ruffus ============================================================== **Let's see if Pweave and ruffus can play…
Jeremy Leipzig
  • 1,914
  • 3
  • 21
  • 26
2
votes
1 answer

Using Ruffus library in Python 2.7, just_print flag fails

I've got a ruffus pipeline in Python 2.7, but when I call it with -n or --just_print it still runs all the actual tasks instead of just printing the pipeline like it's supposed to. I: * don't have a -n argument that would supercede the built-in…
J. C. Szamosi
  • 23
  • 3
2
votes
1 answer

How to use subdirectories with Ruffus pipelines

The Ruffus pipeline documentation seems to assume that one's code and data are in the same directory. All the examples have input and output file specifiers without any relative paths. How should one modify the syntax below if, say, the files to be…
Quant
  • 23
  • 5
1
vote
1 answer

Ruffus pipeline with internal inputs

I'd like to create a pipeline with the Ruffus package for Python and I am struggling with its simplest concepts. Two tasks should be executed one after the other. The second task depends on output of the first task. In Ruffus documentation…
Damian
  • 79
  • 1
  • 11
1
vote
1 answer

requiring set of files to be made before running function in Ruffus pipeline

I'm using ruffus to write a pipeline. I have a function that gets called in parallel many times and it creates several files. I'd like to make a function "combineFiles()" that gets called after all those files have been made. Since they run in…
user248237
0
votes
0 answers

How to make a refresh on a var python / Ruffus

I'm new to the field of bioinformatics, and a Python beginner. I'm using a framework called Ruffus to run a pipeline making files navigating through tools to have an interesting output. In a part of my pipeline (3rd step) I need to do a little…
Bratten
  • 31
  • 5