These are chat archives for nextflow-io/nextflow

12th
Apr 2016
Jose Espinosa-Carrasco
@JoseEspinosa
Apr 12 2016 10:01
Hi Paolo!
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:01
Hola
Jose Espinosa-Carrasco
@JoseEspinosa
Apr 12 2016 10:02
Could it be that -resume option is not working properly in latest nf version
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:02
um, I would say that's not possible :)
Jose Espinosa-Carrasco
@JoseEspinosa
Apr 12 2016 10:03
When I use it, it seems to retrieve all process that worked
but not to launch the ones that failed
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:03
it has a different behavior with the previous version ?
Jose Espinosa-Carrasco
@JoseEspinosa
Apr 12 2016 10:05
I don't know, it is just that I updated nf version this morning and I thought it might be related with this
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:06
try to use the previous version by using this command:
NXF_VER=0.17.3 nextflow run ... -resume
Jose Espinosa-Carrasco
@JoseEspinosa
Apr 12 2016 10:06
ok, I'll try!
thanks
Matthieu Foll
@mfoll
Apr 12 2016 10:33
Hi Paolo, a quick follow up on our set -o pipefail issue
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:33
Hi, yes
Matthieu Foll
@mfoll
Apr 12 2016 10:34
it turns out to behave badly sometimes with an error code 141:
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:34
ah, what's the cause of that?
Matthieu Foll
@mfoll
Apr 12 2016 10:35
[follm@hn ~]$ seq 1 100000 | head -1 ; echo $?
1
0
[follm@hn ~]$ set -o pipefail ; seq 1 100000 | head -1 ; echo $?
1
141
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:35
!!
Matthieu Foll
@mfoll
Apr 12 2016 10:36
a head command can interrupt another one, returning error 141
can also happen with grep -q
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:36
so, it's definitely not a good idea to set it as default !
Matthieu Foll
@mfoll
Apr 12 2016 10:36
indeed!
Paolo Di Tommaso
@pditommaso
Apr 12 2016 10:37
Thanks to let me know that
Matthieu Foll
@mfoll
Apr 12 2016 10:38
you're welcome