Nextflow community chat moved to Slack! https://www.nextflow.io/blog/2022/nextflow-is-moving-to-slack.html
R1 = Channel.create()
R2 = Channel.create()
Channel.from(['Sample_a', ['a.R1.fastq', 'a.R2.fastq']]
, ['Sample_b', ['b.R1.fastq', 'b.R2.fastq']]
, ['Sample_c', ['c.R1.fastq', 'c.R2.fastq']])
.separate ( R1, R2 ) { it -> (id, reads) = it; [ [id, reads[0]], [id, reads[1]] ] }
def sortfqlist(thelist) {
thelist
.sort { a,b -> a[0] <=> b[0] }
.collect { it[1] }
}
R1.toList()
.subscribe onNext: { list = sortfqlist(it); println "list1: " + list }
R2.toList()
.subscribe onNext: { list = sortfqlist(it); println "list2: " + list }
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
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?
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?
ch_input = Channel.create()
@pditommaso
this is just great, isn't it ?
https://twitter.com/yokofakun/status/1159468857934929922
Confirmed, this is great
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
Channel.fromMap("my.bam").flatMap(Htsjdk::extractSamples)
