bpipe-discuss

Hi, I don't know if this group is still active or not. But I have a very naive question: how do I

hi, i have the following problem. I created my own pipeline that takes its own cli parameters like so

Simon hi, I must apologize for not thoroughly reading the manual. U understood exactly what I am

Hi Neulhyo, Bpipe doesn't currently provide any specific support for running commands or

Apologies, it was down due to a server relocation, but should be back up again now! Cheers, Simon On

So I've figured out why this: run { [ control * [[qc,trim] + [qc,align.using(type:'control

The closest I've got is something like this: exec """ echo $input ""

Does anyone know if it's possible to use wildcards whilst specifying explicit paths? I have some

I got it working by setting the concurrency in the bpipe.config. I've got the run command in a

Apologies, this is probably something terribly basic, but I haven't been able to figure this out.

Hi, Indeed it can get executed twice. This could probably be made clearer in the documentation: in

There are a few different approaches to that. If you want to do it generically, you can register an

Thanks, that should do nicely. On Fri, Jun 15, 2018 at 4:46 PM, bpipe-discuss on behalf of Simon <

It stayed kind of experimental as I found although it was neat, I still found it better to write

Dear Simon Thanks a lot for the quick answer. Indeed I wanted to avoid a simple produce(*.split)

I have created 2 different version of same pipeline and would like to setup testing framework for it.

Sorry, sent that too early! The example would be: download = { requires r1_input : 'The R1 file

Thanks that helped me a lot to fix the problem On Wednesday, November 8, 2017 at 6:31:24 AM UTC-5,

Anyone have a good resource (documentation or examples) on how to set up a fairly complex pipeline

Hi Simon, Thanks for the response and the code/troubleshooting hints. What we were seeing was the /

Hi I looked a bit further in your code and was wondering. Would it work if I introduce in your Uitls.

Thanks for the input! Indeed it would be unfortunate to have FASTA files for each as I have in total

Hi all, The main site http://docs.bpipe.org/ is working fine for me right now (Melbourne. Australia).

Hi, I found this workflow (https://github.com/vlsci/bpipe-trinotate/blob/master/trinotate.groovy). I

Hi Jiarui, How to pass parameters to a flag accepting multiple values, eg, --m file_one --m file_two

Dear Group, I am trying to run a bpipe pipeline, but am receiving the following error: An error

It did help, thanks! Your guess is probably right, and re-using the variables which already have

Hi, happy to do that. Any chance you can move the recent feature request for slurm options into

NB: did a quick implementation of this in a branch called custom_submit_opts. See Issue #193. Any

Hi Linjun, I have the same problem too. I think the problem is most likely caused by the NFS latency