These are chat archives for nextflow-io/nextflow

30th
May 2018
micans
@micans
May 30 2018 10:52
In the past days, I got used to (1) nextflow pull cellgeni/rnaseq-noqc, (2) nextflow run cellgeni/rnaseq-noqc(3) changing things in my $HOME/.nextflow/assets/cellgeni/rnaseq-noqc directory and subsequently repeating (2) and (3). I now want to test the branch scratchfiles. I can pull and run this branch with -r scratchfiles, but if I now change something in the assets directory, I get this message: Project cellgeni/rnaseq-noqc contains uncommitted changes. The assets directory is on the right branch scratchfiles; I've tried dropping -r scratchfiles from the run step but that gives a sticked on revision error and advises me to use the -r branch.
Paolo Di Tommaso
@pditommaso
May 30 2018 11:26
you are not supposed to make changes in that dir, if you do you need to commit or revert them
micans
@micans
May 30 2018 11:27
OK, fair enough. It seems to work the way I described it for master, and not for branches (and it makes for quick testing) but your answer is very clear. Thanks!
Luca Cozzuto
@lucacozzuto
May 30 2018 14:45
hi all
there is a way to extract only a part of string in a channel?
i.e. I have a channel with
[QC01_180308_Q_QC1X_01_02, [/nfs/software/bi/biocore_tools/git/nextflow/Qcloud/test_data/QC01_180308_Q_QC1X_01_02.mzML.gz]]
[QC01_180308_Q_QC1X_01_01, [/nfs/software/bi/biocore_tools/git/nextflow/Qcloud/test_data/QC01_180308_Q_QC1X_01_01.mzML.gz]]
[QC01_180308_Q_QC1X_01_03, [/nfs/software/bi/biocore_tools/git/nextflow/Qcloud/test_data/QC01_180308_Q_QC1X_01_03.mzML.gz]]

I would like to have

[QC01,QC01_180308_Q_QC1X_01_02, [/nfs/software/bi/biocore_tools/git/nextflow/Qcloud/test_data/QC01_180308_Q_QC1X_01_02.mzML.gz]]

etc

Maxime Garcia
@MaxUlysse
May 30 2018 14:48
You might want to look into map to remap your channel
Luca Cozzuto
@lucacozzuto
May 30 2018 14:49
how to "extract " the first code?
Maxime Garcia
@MaxUlysse
May 30 2018 14:49
I'm guessing the QC01 is just the begining of your id wich is the first value ?
Luca Cozzuto
@lucacozzuto
May 30 2018 14:50
yes
Maxime Garcia
@MaxUlysse
May 30 2018 14:50
have you looked into substring
Luca Cozzuto
@lucacozzuto
May 30 2018 14:50
something to "split"
Luca Cozzuto
@lucacozzuto
May 30 2018 14:51
yes I was
but not so easy because of channels
Maxime Garcia
@MaxUlysse
May 30 2018 14:53
Luca Cozzuto
@lucacozzuto
May 30 2018 14:54
how to deal with channels..
Maxime Garcia
@MaxUlysse
May 30 2018 14:55
I would try something like:
channel.map{
  value, file ->
  value.split('_')[0], value, file
}
Luca Cozzuto
@lucacozzuto
May 30 2018 15:02
channel.map{
  value, file ->  [value.split('_')[0], value, file]
}
Venkat Malladi
@vsmalladi
May 30 2018 15:03
+1
Luca Cozzuto
@lucacozzuto
May 30 2018 15:03
this it works
thanks a lot!
Maxime Garcia
@MaxUlysse
May 30 2018 15:03
np
Glad I could help
And I'm also happy that it looks a little like a smiley ('_')[0]
Luca Cozzuto
@lucacozzuto
May 30 2018 15:06
:)))
LukeGoodsell
@LukeGoodsell
May 30 2018 16:30

Hi, I’m having trouble launching nextflow processes on aws batch. The job seems to get launched, but fails with:

/usr/local/bin/docker-entrypoint.sh: exec: line 35: bash: not found

in the job log.
Any suggestions?

Paolo Di Tommaso
@pditommaso
May 30 2018 16:33
what is producing this error ?
LukeGoodsell
@LukeGoodsell
May 30 2018 16:36
I have a very basic nextflow script that just echos a value to a file. I’m trying to get it to run on awsbatch, though. That error message is from the aws batch log (CloudWatch > Log Groups >/aws/batch/job)
Paolo Di Tommaso
@pditommaso
May 30 2018 16:37
what's the container image you are using ?
LukeGoodsell
@LukeGoodsell
May 30 2018 16:38
docker://nextflow/rnaseq-nf
Paolo Di Tommaso
@pditommaso
May 30 2018 16:40
how is the nextflow.config file ?
LukeGoodsell
@LukeGoodsell
May 30 2018 16:45
I haven’t created/modified nextflow.config - my aws credentials are in ~/.aws and my process has these config parameters:
    executor "awsbatch"                                                         
    container "docker://nextflow/rnaseq-nf"                                     
    queue "first-run-job-queue”
and I have ‘-w s3://BUCKET/nftest' on the command line
Paolo Di Tommaso
@pditommaso
May 30 2018 16:46
docker://nextflow/rnaseq-nf is not a valid docker image name, it should be nextflow/rnaseq-nf
LukeGoodsell
@LukeGoodsell
May 30 2018 16:51
Ahh, thanks. But now I get:
Screen Shot 2018-05-30 at 17.51.22.png
blue box
LukeGoodsell
@LukeGoodsell
May 30 2018 16:54
So aws isn’t in the nextflow/rnaseq-nf image? I’d just assumed it was
Paolo Di Tommaso
@pditommaso
May 30 2018 16:54
no, it isn't
LukeGoodsell
@LukeGoodsell
May 30 2018 16:54
okey doke. thanks
Paolo Di Tommaso
@pditommaso
May 30 2018 16:55
:+1: