run jaffa with bioconda in parallel

[ninn...@gmail.com]

Hi there,

I have managed to run Jaffa with the bioconda installation. However, I have a few questions. This is my current command, which is running:

jaffa-assembly chroms/hg38.fa Edgren/BT-474_*.fastq.gz 

But I would like to add

- number of threads

- memory usage

- outpu folder

What confused me the most was that setting genomeFasta=path and fastqInputFormat would not work. Only leaving the variable out the call is running. Is it supposed to be like this? 

Any help is highly appreciated. 

Thank you!

Nina

[Nadia Davidson]

Hi Nina,

I haven't been involved in the bioconda version of jaffa (it's very cool by the way that someone has written a recipe for it!), but it looks like the bioconda version doesn't take the settings:

In the line below in the recipe, the setting would have been passed as a variable between "run" and the groovy pipeline file.

bpipe run $TMPDIR/JAFFA_$RUNMODE.groovy $*

I'll forward to the bioconda author for comment.

Cheers,

Nadia.