These are chat archives for nextflow-io/nextflow

18th
Aug 2015
Matthieu Foll
@mfoll
Aug 18 2015 12:37
Hi Paolo,
I have a small issue with github pipeline sharing. I can pull the pipeline once, but if I want to pull it again (after updating it for example) I always have the error:
"contains uncommitted changes -- cannot pull from repository”
I need to manualy delete it in .nextflow/assets and then I can pull it again.
Any idea where this comes from? If you want to check, the pipeline is mfoll/robust-regression-caller on github
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:40
Hi Matthieu, that means that some file in pipeline repository has been modified
is this the repo?
Matthieu Foll
@mfoll
Aug 18 2015 12:41
yes
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:43
it seems fine
what if you change to $HOME/.nextflow/assets/mfoll/robust-regression-caller
and run git status ?
Matthieu Foll
@mfoll
Aug 18 2015 12:45
On branch master
Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    deleted:    pileup2base

no changes added to commit (use "git add" and/or "git commit -a”)
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:46
ah
I've never tested with a git submodule
Matthieu Foll
@mfoll
Aug 18 2015 12:46
indeed it seems to be the problem here
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:47
yes, because it need an extra command to be handled correctly
would you like to open a issue for that?
Matthieu Foll
@mfoll
Aug 18 2015 12:48
ok
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:48
anyway great job with your pipeline
Matthieu Foll
@mfoll
Aug 18 2015 12:48
thanks
the integration of nextflow with docker makes it so easy to run
and to develop and maintain too
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:50
I'm very proud about that :)
Matthieu Foll
@mfoll
Aug 18 2015 12:51
Just another quick question: is it on purpose that when using shell in processes I still need to backslash the backslashes? Like writing \n or \t?
Paolo Di Tommaso
@pditommaso
Aug 18 2015 12:53
umh, good point
no it's not on purpose, but I need to investigate if they can be omitted.
If I'm not asking to much you could open a issue also for that showing an example for your use case
Matthieu Foll
@mfoll
Aug 18 2015 12:56
ok sure
Paolo Di Tommaso
@pditommaso
Aug 18 2015 13:07
@mfoll I've added your pipeline to this list
hope it is fine for you
Matthieu Foll
@mfoll
Aug 18 2015 13:08
Sure. I will soon update the readme to describe what it is doing...
Matthieu Foll
@mfoll
Aug 18 2015 13:26
Ok I just noticed that not all backslashes have to be backslashed… I’m opening an issue, you’ll see with my toy example.
Paolo Di Tommaso
@pditommaso
Aug 18 2015 13:27
ok thanks
Matthieu Foll
@mfoll
Aug 18 2015 14:04
btw, as you looked at my nf script, don’t hesitate to tell me if you see some bad practices in there or things that could me done in a better way!
Paolo Di Tommaso
@pditommaso
Aug 18 2015 14:06
I did :)
it looks pretty good
in any case if I have suggestions I will let you know