Issues with naming in Ruffus

[Collioure]

Hi,

I hope this forum is still active.

My group is using Ruffus to run pipelines, and I definitely have troubles in understanding how ruffus deals with names.

It seems that depending on the decorator (@transform versus @subdivide), the name expected is different, and that is very surprising.

It seems if my stages 1, 2 and 3 have : 

1 : input : _appl.vcf output : _flqg.vcf

2 : input : .vcf output : .avinput

3 : input : .avinput output : _1000G_filter

If stage 2 is  @subdivide (because my stage 2 is basically giving 2 output for 1 input) the file name expected is : *.appl_flqg.avinput and when I use @transform it's *.appl.vcf_filqg.vcf.avinput

That's a huge difficulty then to be able to run a pipeline if the names are not expected to be the same.

My stage 2 uses a software that changes the filename (let's say it adds a part of my samples name in the output file), I have to hack it, by doing a glob on the files by myself, but it seems that ruffus loads all the var in the function at the beginning, so it's pretty hard to re-load the filelist when launching the script. (Basically I have to relaunch the script from the beginning each time)

The documentation is for me quite unclear, can you give me clear examples about how to deal with that? 

Best,

[Valentin Krasontovitsch]

Hi there,

I think based on the pinned posts and recent activity it is quite safe to say that the mailing list is dead. I myself just came to get a confirmation of that hunch... of course is rather counterproductive to write something, in that case, but oh well : )

It's a bit hard for me to follow your example / understand your problem.

Perhaps you could publish a minimal working example that illustrates the behaviour you're observing? That would make it much more feasible for others to help you!

Cheers,
Valentin