These are chat archives for nextflow-io/nextflow

15th
Jun 2018
Bioninbo
@Bioninbo
Jun 15 2018 07:32
Maybe it could help to make a new pattern for the saveAs command in section Organizing Output; eg:
  saveAs: {filename ->
         if (filename.indexOf(".csv") > 0) "csv/$filename"
         else if (filename.indexOf(".bed") > 0) "bed/$filename"
          else "rda/$filename"
            }
Paolo Di Tommaso
@pditommaso
Jun 15 2018 07:33
sounds good, feel free to send a PR
micans
@micans
Jun 15 2018 09:13
Can I check, the disk directive, on LSF does that refer to tmp storage?
Paolo Di Tommaso
@pditommaso
Jun 15 2018 09:16
I would say it does nothing with LSF
if you want to propose an implementation you are welcome
micans
@micans
Jun 15 2018 09:18
Useful, thanks! Maybe when I have moved beyond novice. For now I'll use clusterOptions.
Paolo Di Tommaso
@pditommaso
Jun 15 2018 09:22
how is the LSF option for that ?
micans
@micans
Jun 15 2018 09:25
Checking some very old notes ... it says -R 'rusage[mem=60000 && tmp>60000]
so similar to mem. I'm not sure I've ever used it but it looks legitimate. IBM documentation mentions tmp as well.
Paolo Di Tommaso
@pditommaso
Jun 15 2018 09:27
ok, if so please open an issue to remind me to add that in the lsf executor
micans
@micans
Jun 15 2018 09:28
:+1:
sorry for spam, but maybe there are some good people here
hope this is ok
Paolo Di Tommaso
@pditommaso
Jun 15 2018 10:10
you are very welcome
Vladimir Kiselev
@wikiselev
Jun 15 2018 10:10
:+1:
Félix C. Morency
@fmorency
Jun 15 2018 14:33
Are some of you going to ISMRM?
Alexander Peltzer
@apeltzer
Jun 15 2018 14:54
ISMB
Paolo Di Tommaso
@pditommaso
Jun 15 2018 14:59
where's ISMB this year ?
Alexander Peltzer
@apeltzer
Jun 15 2018 15:00
Chicago
July 5-11th
Paolo Di Tommaso
@pditommaso
Jun 15 2018 15:00
:+1:
are you going to present ?
Alexander Peltzer
@apeltzer
Jun 15 2018 15:03
Yes, bioinfo Core workshop
Nf Core / Nextflow
Paolo Di Tommaso
@pditommaso
Jun 15 2018 15:03
:v: :v: :v:
Félix C. Morency
@fmorency
Jun 15 2018 15:07
I don't know what I expected asking a bioinformatic croud... :D
Paolo Di Tommaso
@pditommaso
Jun 15 2018 15:08
lol
you should join compbio :wink:
Félix C. Morency
@fmorency
Jun 15 2018 15:09
I'm sure there are overlaps (other than the use of NF) between our fields
Paolo Di Tommaso
@pditommaso
Jun 15 2018 15:09
I guess so