Next step do not wait previous one

GoogleCodeExporter commented 9 years ago

Hi everybody,

I run bpipe with a program that do no allow to specify an output. I thus do not 
have $output in the command line of this first step.

This program procude 2 files, and I need both for next step.
But next step starts when only one file is generated... As it doesn't know 2 
files will be produced, it takes the first to be completed....

Can I have a wait to force the next step to wait for the first one has really 
terminated its job ?

I thought about requires but it's not clear... I tried with:
requires input.prefix-trimmed-pair2.fastq
but it seems it believed .fastq is calling a class.....

Thanks a lot

Original issue reported on code.google.com by fabien.p...@gmail.com on 8 Apr 2015 at 12:42

GoogleCodeExporter commented 9 years ago

[deleted comment]

GoogleCodeExporter commented 9 years ago

Hum...I am not really sure it's what is indeed happening...
I have to check it more closely...

It seems that in the next step, bowtie is rewriting my fastq file...

Original comment by fabien.p...@gmail.com on 8 Apr 2015 at 1:26

GoogleCodeExporter commented 9 years ago

Ok, it was my mistake, sorry. It waits for both files and starts with both 
files.
Thanks for this very useful tool !

Original comment by fabien.p...@gmail.com on 9 Apr 2015 at 2:18

pallassgj / bpipe

Next step do not wait previous one #109