These are chat archives for nextflow-io/nextflow

22nd
Oct 2015
Rahul
@RahulReddy75
Oct 22 2015 14:26
hi,how are large reads split and merged in nextflow... these chunks should go through multiple process like bwa, bowtie readmapper etc and the finally these processed chucks must be merged to a out put file... is this process possible? the example in git hub has just a single blast process...
Paolo Di Tommaso
@pditommaso
Oct 22 2015 15:08
@Rahul1992 it depends on the logic of your pipeline, you can split the reads with a tool like Picard or use the nextflow method splitFastq
Also try to give a look at the examples at this page
Rahul
@RahulReddy75
Oct 22 2015 15:10
ok i will try to take a look into the examples.
i actually have an error popping up when i run the split_fasta.nf
the error say the Process 'blast (1)' terminated with an error exit status
Paolo Di Tommaso
@pditommaso
Oct 22 2015 15:13
likely there's an error :)
Rahul
@RahulReddy75
Oct 22 2015 16:03
yeah.. i do not know how to debug the blast process.
Paolo Di Tommaso
@pditommaso
Oct 22 2015 18:10
That's easy. When there's an error nextflow stops reporting at the end of the error message the directory where your task was executed. For example:
:
Work dir:
  /Users/pditommaso/projects/work/ad/16f5ba8217887b05d1182bc3df299d
Change to that directory, your task is in a script named .command.sh
you can execute and debug it, writing bash -x .command.sh
enjoy