These are chat archives for nextflow-io/nextflow

11th
Mar 2016
Tiffany Delhomme
@tdelhomme
Mar 11 2016 14:06

Hello,
I get this error

Launching ./bam_realignment.nf
ERROR ~ startup failed:
bam_realignment.nf: 45: expecting '}', found ',' @ line 45, column 37.
       file("${bam_tag}_realigned.bam"), file("${bam_tag}_realigned.bam.bai") into outputs

I just would like to output these two files...
my output is:

output:
    file("${bam_tag}_realigned.bam"), file("${bam_tag}_realigned.bam.bai") into outputs

thanks in advance

Tiffany Delhomme
@tdelhomme
Mar 11 2016 15:29
Actually if I add into output set val(bam_tag) it works, yes I need to output this variable...
Paolo Di Tommaso
@pditommaso
Mar 11 2016 15:32
sorry, I didn't get if you manage to solve the problem
Tiffany Delhomme
@tdelhomme
Mar 11 2016 16:18

Yes I did:
This does not work:

output:
    file("${bam_tag}_realigned.bam"), file("${bam_tag}_realigned.bam.bai") into outputs

But this does:

output:
    set val(bam_tag), file("${bam_tag}_realigned.bam"), file("${bam_tag}_realigned.bam.bai") into outputs

But is the reason because we have to output the tag if we want to output file named by the tag?

Paolo Di Tommaso
@pditommaso
Mar 11 2016 16:20
no, the reason is that whenever you need to output multiple items, you will need a set ... clause in the output definition
Jason Byars
@jbyars
Mar 11 2016 18:48
What determines the polling rate to check that jobs are complete when you use a pbs executor?
Paolo Di Tommaso
@pditommaso
Mar 11 2016 18:57
@jbyars The config property pollInterval in the executor config
Default should be 4 min 30 secs
Jason Byars
@jbyars
Mar 11 2016 18:58
great, I'll give that a try. It looks like Jenkins must think the jobs are lingering on for other reasons.
Jason Byars
@jbyars
Mar 11 2016 19:58
ahh, I think I see my problem. There are errors looking for the shared home directory. What is the proper way to specify where the shared directory for work should be located?
Paolo Di Tommaso
@pditommaso
Mar 11 2016 19:58
ah!
both the -w command line option or NXF_WORK env variable
Jason Byars
@jbyars
Mar 11 2016 20:13
That fixes it. Thanks!
Paolo Di Tommaso
@pditommaso
Mar 11 2016 20:13
Welcome!