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    jfy133 review_requested #3589
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Stijn van Dongen
@micans
it's powerful love
Paolo Di Tommaso
@pditommaso
the best one
Stijn van Dongen
@micans
I know, reminds me of that year there were three songs all called the 'the power of love'
Huwey Lewis and the News, Jennifer Rush, and Frankie goes to Hollywood IIRC
Paolo Di Tommaso
@pditommaso
lol
Seth
@sstadick
Hi! Is there any documentation surrounding the -params-file option? I see it referenced in old issues, and kicking around in the source code, but it doesn't look like it's used anymore?
Tobias "Tobi" Schraink
@tobsecret
@sstadick I typically write bash scripts that run nextflow with params specified
Paolo Di Tommaso
@pditommaso
Just specify a yaml or json file
Seth
@sstadick
:thumbsup: I didn't realize it was going to be that simple.
Paolo Di Tommaso
@pditommaso
:stuck_out_tongue_closed_eyes:
Shellfishgene
@Shellfishgene
@micans Thanks for the update!
Chadi Saad
@chadisaad
Good morning ! How can I get easly for a specific nextflow job, the list of all child process (executed via slurm) ?
Pierre Lindenbaum
@lindenb
following this conversation on twitter with @pditommaso ( https://twitter.com/yokofakun/status/1159072968158457856 ) I'm trying to implement some new operators. It's not the final design of the source, (I don't think using the notation 'splitter' is a good choice because we don't really read any line). However , it doesn't work.
I implemented a splitter: https://github.com/lindenb/nextflow/blob/pl_htsjdk_op/modules/nextflow/src/main/groovy/nextflow/extension/htsjdk/SamplesSplitter.groovy
I use this splitter in OperatorExt : https://github.com/lindenb/nextflow/blob/pl_htsjdk_op/modules/nextflow/src/main/groovy/nextflow/extension/OperatorEx.groovy#L1623
I compile './gradlew build -x test ` and when I want to run, I get the following error:
 cat test.nf 
Channel.fromPath("/home/lindenb/src/jvarkit-git/src/test/resources/toy.bam").
    splitSamples().
    dump()
$ ./nextflow run test.nf
N E X T F L O W  ~  version 19.08.0-SNAPSHOT
Launching `test.nf` [goofy_goldstine] - revision: f56eb762e4
Unknown method `splitSamples` on channel type
NF cannot find my operator. what am i missing in the code ?
Vũ Mạnh Tú
@glmanhtu

Hello guys. I'm trying to run nextflow with Kubernetes and have encountered some sort of problem with non-root user. Nextflow was trying to initialise a Pod but got an exception of "container init caused \"mkdir /mnt/tvu: permission denied". Below is the Kubernetes manifest generated by nextflow:

apiVersion: v1
kind: Pod
metadata:
  name: nf-68b883e7affa9dc5d6d5e721c75b21c4
  namespace: default
  labels: {app: nextflow, runName: sleepy-goodall, taskName: indexPeptides, processName: indexPeptides,
    sessionId: uuid-0e5b6c81-4527-4213-a9ba-16e40e424220}
spec:
  restartPolicy: Never
  containers:
  - name: nf-68b883e7affa9dc5d6d5e721c75b21c4
    image: omicsdi/crux:latest
    command: [/bin/bash, -ue, .command.run]
    workingDir: /mnt/tvu/work/68/b883e7affa9dc5d6d5e721c75b21c4
    volumeMounts:
    - {name: vol-1, mountPath: /mnt}
  securityContext: {runAsUser: 2801}
  volumes:
  - name: vol-1
    persistentVolumeClaim: {claimName: pride-pv-claim}

I have assigned rw permission to the persistent volume. When I removed the workingDir, the pod was started successfully and I was be able to cd into the /mnt/tvu/work/68/b883e7affa9dc5d6d5e721c75b21c4 folder. So, I suspect that the runAsUser and workingDir couldn't get along.
Is there anyone have experienced this issue?

Paolo Di Tommaso
@pditommaso
@lindenb try using ./launch.sh instead of nextflow script
then much simpler to test it using a test class
have a look at this example
and the invocation as operator
I would suggest also to open a draft pull request and keep a discuss thread there
Pierre Lindenbaum
@lindenb
@pditommaso :thumbsup:
Philip Jonsson
@kpjonsson
Question: In Nextflow version 19.07.0.5106, I get WARN: The channelcreatemethod is deprecated -- it will be removed in a future release when I use the Channel.create() method, but I find nowhere any mention of what's replacing it. Is the warning wrong or is there some undocumented feature I'm missing?
Ghost
@ghost~57581dbcc2f0db084a1ccd04
Don't worry, it won't happen overnight
AFAIK you can safely already remove the stuff like ch_input = Channel.create()
Philip Jonsson
@kpjonsson
@MaxUlysse Got it, thanks.
Ghost
@ghost~57581dbcc2f0db084a1ccd04

And I do believe that was the important part:

to me the only use for create that makes sense is when used with choice

Paolo Di Tommaso
@pditommaso
this is just great, isn't it ?
Hugues Fontenelle
@huguesfontenelle
hi!
How do I read the documentation for an older release? ie 19.04
well I guess I can simply read in github ..
Paolo Di Tommaso
@pditommaso
indeed
evanbiederstedt
@evanbiederstedt

@pditommaso
this is just great, isn't it ?
https://twitter.com/yokofakun/status/1159468857934929922

Confirmed, this is great

evanbiederstedt
@evanbiederstedt

https://gitter.im/nextflow-io/nextflow?at=5d4802a1475c0a0feb021c1b

Could you give us a few examples @pditommaso to illustrate this point? It still feels a bit abstract without a few concrete examples

Pierre Lindenbaum
@lindenb
@evanbiederstedt @pditommaso thanks ! I'm still not convinced it's the right way to implement the idea. 1) one can still use a bash script to extract the data 2) or it would be better using a 'static' method: something like:Channel.fromMap("my.bam").flatMap(Htsjdk::extractSamples)
Taylor Falk
@taylor.f_gitlab
Is there an easy way to pass two channel outputs and some associated strings to a process? I'm currently trying output = Channel.from(['filter1', channel1_out], ['filter2', channel2_out]) but this only returns the blank DataflowQueue(queue=[]) string inside the process.
Stijn van Dongen
@micans
@taylor.f_gitlab that would mean you'd have channels in a channel. What are you trying to achieve? What's in channel1_out and channel2_out?
Taylor Falk
@taylor.f_gitlab
@micans those channels contain singular files, so I am really just trying to run the next process on each output from channel1 and channel2, and passing along the correct filter string. How do I move those files into one channel, concat?
Stijn van Dongen
@micans

@taylor.f_gitlab do you have a source process? Normally you'd see something like

output: set val('filter'), file('*.txt') into channel1

then if there are multiple files in that output that you want to flatten you can use transpose().

Taylor Falk
@taylor.f_gitlab
Oh that's a good idea, let me try it that way.
Gabriel Abud
@G_Abud_twitter
I'm getting the error: fatal error: An error occurred (AccessDenied) when calling the ListObjectsV2 operation: Access Denied when trying to run a pipeline on AWS Batch. Pretty sure it's due to the s3 access of the workDir but I've double checked and I am the owner of that bucket. Any ideas?
Combiz
@combiz_k_twitter
Hi, this may be more of a singularity question than a nextflow one. I'm trying to run a test hello world nextflow script with -with-singularity image.sif on an HPC cluster. There seems to be an issue with mounting as the short script runs but produces an error `Command error: Fatal error: cannot create 'R_TempDir'. Any ideas? My guess is the singularity container can't write files to the HPC filesystem? Thanks for any pointers.
Combiz
@combiz_k_twitter
Ok so the script now runs with containerOptions '-B $PWD:/tmp' in the process
Johannes Alneberg
@alneberg

A question regarding input of memory specifications. Using the config

params {
  memParam = 7.GB
}

process {
  withName:sayHello {
    memory = {2 * params.memParam}
  }
}

works fine when memParam is not used, but when it is: nextflow run main.nf -c base.conf --memParam 8.GB, I get either

ERROR ~ Error executing process > 'sayHello (3)'

Caused by:
  No signature of method: java.lang.Integer.multiply() is applicable for argument types: (java.lang.String) values: [8.GB]
Possible solutions: multiply(java.lang.Character), multiply(java.lang.Number)

or

Error executing process > 'sayHello (1)'

Caused by:
  Not a valid 'memory' value in process definition: 8.GB8.GB

depending on the order of the multiplication. What am I missing? (I'm on Nextflow version 19.04.1 build 5072)

Paolo Di Tommaso
@pditommaso
umm, because when passing on the command line the string 8.GB does not get parse to Memory unit object
therefore for the interpreter it's a string
Johannes Alneberg
@alneberg
Is it possible to go around?