These are chat archives for nextflow-io/nextflow

21st
Sep 2018
Crabime
@Crabime
Sep 21 2018 09:56
why nextflow generated .command.stub etc files without execute permission? here i run a process in docker container and get error /bin/bash xxx/.command.stub: permission denied
I execute such script using root and run in SGE cluster
Luca Cozzuto
@lucacozzuto
Sep 21 2018 11:27
Hi all. I changed an input file within my nextflow pipeline but when I did resume it still give me "cached process"... what is happening?
Paolo Di Tommaso
@pditommaso
Sep 21 2018 12:12
likely your file is not really an input :D
Luca Cozzuto
@lucacozzuto
Sep 21 2018 12:30
mmm
let me guess
not in a channel != not an input?
Paolo Di Tommaso
@pditommaso
Sep 21 2018 12:32
it must be in some file: input x from <your file>
Alexander Peltzer
@apeltzer
Sep 21 2018 14:07

something like .groupTuple(~/^.*_(L[0-9]+)_.*\.fastq\.gz/)

ERROR ~ No signature of method: groovyx.gpars.dataflow.DataflowQueue.groupTuple() is applicable for argument types: (java.util.regex.Pattern) values: [^.*_(L[0-9]+)_.*\.fastq\.gz] Possible solutions: groupTuple(java.util.Map)

Hmm, I guess I'll have to find another way
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:09
oops, I mean Channel.fromFilePath but I don't remember what you really need
Alexander Peltzer
@apeltzer
Sep 21 2018 14:17
https://github.com/apeltzer/RNAseq/blob/0c58551f7246529647f81bb74bc8c02452d1a08c/main.nf#L462
I already have a channel with reads in there, but want to glob the ones spread across multiple lanes together :-)
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:24
umm .. something channel.map { it -> [ extractYourKeyLogic(it), it ] } .groupTuple()
Luca Cozzuto
@lucacozzuto
Sep 21 2018 14:40
paolo is java 1.10 working with nextflow?
because it complains
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:41
what is complaining ?
Luca Cozzuto
@lucacozzuto
Sep 21 2018 14:42
that 1.8 is missing
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:42
error message ?
Luca Cozzuto
@lucacozzuto
Sep 21 2018 14:44
Unable to find any JVMs matching version "1.8".
Julia installed java in her Mac and it is complaining about the java
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:46
user latest version of NF
Luca Cozzuto
@lucacozzuto
Sep 21 2018 14:49
is the latest
she just donwloaded it
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:55
$ java -version
java version "10" 2018-03-20
Java(TM) SE Runtime Environment 18.3 (build 10+46)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10+46, mixed mode)

$ nextflow info
  Version: 0.31.1 build 4886
  Modified: 07-08-2018 15:53 UTC (17:53 CEST)
  System: Mac OS X 10.11.6
  Runtime: Groovy 2.4.15 on Java HotSpot(TM) 64-Bit Server VM 10+46
  Encoding: UTF-8 (UTF-8)
Luca Cozzuto
@lucacozzuto
Sep 21 2018 14:56
she downloaded the latest version today from the website..
mmm
Julias-MacBook-Pro:vectorQC jpon$ nextflow -version
Unable to find any JVMs matching version "1.8".

      N E X T F L O W
      version 0.31.1 build 4886
      last modified 07-08-2018 15:53 UTC (17:53 CEST)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

Julias-MacBook-Pro:vectorQC jpon$ which java
/usr/bin/java
Julias-MacBook-Pro:vectorQC jpon$ java -version
java version "10.0.2" 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)​
Paolo Di Tommaso
@pditommaso
Sep 21 2018 14:59
use nextflow -self-update and try again
Luca Cozzuto
@lucacozzuto
Sep 21 2018 15:05
the warning is still there
shake a dead chicken over the screen
Luca Cozzuto
@lucacozzuto
Sep 21 2018 15:09
only if singing "quanto sei bella roma"
tbugfinder
@tbugfinder
Sep 21 2018 17:14
a little bit off-topic, do you know a groovy syntax checker for a pre-commit hook of script files?