These are chat archives for nextflow-io/nextflow

27th
Aug 2018
Karin Lagesen
@karinlag
Aug 27 2018 07:45
so... question re getting git info out in log.info text
I run
if (workflow.commitId) {
version = "v0.2.0 $workflow.repository - $workflow.revision [$workflow.commitId]"
}
else {
version = "v0.2.0 local"
}
however, I never get anything else but the local one, and not the one with git commitids
Shellfishgene
@Shellfishgene
Aug 27 2018 09:16
What does clean actually remove when I select a single run with -but? I have a pipeline for mapping, first it makes the index and then maps the samples. I have stopped and resumed this a few times, the indexes were only created once in the first run. Now if I do clean -but lastest_run it also deletes the indexes? Even if they were also used in the latest run?
Paolo Di Tommaso
@pditommaso
Aug 27 2018 10:55
@karinlag the workflow.repository is only reported if you are specifying a repo name, not the script file path
Paolo Di Tommaso
@pditommaso
Aug 27 2018 11:03
@Shellfishgene it should delete all tasks except the one of the run specified
Shellfishgene
@Shellfishgene
Aug 27 2018 11:03
You mean all files that are newly generated in that run are kept, not the ones that are cached from previous runs?
Paolo Di Tommaso
@pditommaso
Aug 27 2018 11:05
no, are retained all files that concur the execution, including the cached
chdem
@chdem
Aug 27 2018 12:34
Hello ! I'm looking for a way to launch a process with one of its channel that could be empty (not all the time, only in some cases)
Paolo Di Tommaso
@pditommaso
Aug 27 2018 12:35
but ?
chdem
@chdem
Aug 27 2018 12:35
unfortunately, this method allows to launch a process with a channel that is constantly empty
Paolo Di Tommaso
@pditommaso
Aug 27 2018 12:36
I don't think so
chdem
@chdem
Aug 27 2018 12:37
ok
then I have a problem elsewhere, I look in more detail
:D
Karin Lagesen
@karinlag
Aug 27 2018 14:01
@pditommaso hmmm... ok, not sure I understand, but, shouldn't workflow.commitId give something at least? I get a null on all three
and I do have things under version control
Guillaume Theaud
@GuillaumeTh
Aug 27 2018 16:04
Hi, I would like to know which option is used in slurm behind the queue option in nextflow ?
Guillaume Theaud
@GuillaumeTh
Aug 27 2018 16:20
Ok yes thanks, so I have an other question. On a big cluster, I can ask 3 nodes for example and I would like use these 3 nodes with the slurm executor. Is it possible ? If yes how to do that ?
Kevin Sayers
@KevinSayers
Aug 27 2018 16:28
I am not sure I understand the question. You have a slurm cluster and you want to specify 3 specific nodes? or just to use only 3 nodes?
Guillaume Theaud
@GuillaumeTh
Aug 27 2018 16:29
I want to specify 3 specific nodes
Kevin Sayers
@KevinSayers
Aug 27 2018 17:10
https://www.nextflow.io/docs/latest/process.html?highlight=clusteroptions#clusteroptions should allow you to specify other cluster options, I think with -w you could specify the nodes. Not something I have hands on experience with, so someone else may have a better idea.
Guillaume Theaud
@GuillaumeTh
Aug 27 2018 17:14
ok thanks