These are chat archives for nextflow-io/nextflow

14th
Jul 2017
Félix C. Morency
@fmorency
Jul 14 2017 13:37
About this Java8 thing... It's unfortunate for us because Java8 is not on Ubuntu 14.04 and we're all on Ubuntu 14.04 here :(
Paolo Di Tommaso
@pditommaso
Jul 14 2017 13:52
too bad, what about here
Félix C. Morency
@fmorency
Jul 14 2017 14:01
It's possible but uses some user-defined ppa. The latest release in the openjdk ppa date Nov 2016
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:02
what about downloading the Oracle Java from the Oracle web site ?
or
that has it and seems to be active
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:05
Why Oracle Java 7 And 6 Installers No Longer Work
so, also Java 7 is not working ?
Félix C. Morency
@fmorency
Jul 14 2017 14:06
OpenJDK 7 is available on 14.04
But yeah I guess I could use the webupd8 ppa for oracle java 8
We can't stop progress :D
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:08
exactly !
Félix C. Morency
@fmorency
Jul 14 2017 14:09
Migrating to 16.04 is also an option but it seems to be a PITA because systemd
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:09
what's the problem with systemd ?
Félix C. Morency
@fmorency
Jul 14 2017 14:09
everything?
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:10
ahah
maybe time to migrate to Linuxkit :D
Félix C. Morency
@fmorency
Jul 14 2017 14:10
I need to rewrite all our deployment script to support it. When I tested, the official munge package was broken on 16.04 because of systemd
Félix C. Morency
@fmorency
Jul 14 2017 14:32
when do you plan on deprecating java7?
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:32
let's say October
Félix C. Morency
@fmorency
Jul 14 2017 14:37
nice
Shellfishgene
@Shellfishgene
Jul 14 2017 14:52
What does this error mean exacly? A DataflowVariable can only be assigned once. Only re-assignments to an equal value are allowed.
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:53
that you can assign only once ..
what is generating that error ?
Shellfishgene
@Shellfishgene
Jul 14 2017 14:53
Ok, rephrased: How would I find out which variable is responsible?
Paolo Di Tommaso
@pditommaso
Jul 14 2017 14:54
that is the complete error message ?
Shellfishgene
@Shellfishgene
Jul 14 2017 14:54
No, there is also ERROR ~ No such variable: pair_id. Does that mean it's the same variable?
Félix C. Morency
@fmorency
Jul 14 2017 14:55

In my nextflow.config, I have

params {
    foo = [
        'bar': [
            'key1': 10,
            'key2': 20
        ]
    ]
}

Is it possible to change the value of key1 directly from the command line?

Shellfishgene
@Shellfishgene
Jul 14 2017 14:55
ah, the assignment error is gone now, hmm. I removed .ifEmpty ... from the channel creation.
Paolo Di Tommaso
@pditommaso
Jul 14 2017 19:29
@fmorency nope
Shawn Rynearson
@srynobio
Jul 14 2017 20:59
New to Nextflow and I have a processing question. If I point a channel at a directory that has say 100 fastq files in it, but I don't want the workflow to co-process all 100 at the same time (both local and cluster) is their a way to throttle the rate?
Mike Smoot
@mes5k
Jul 14 2017 21:19
@srynobio check out the maxForks directive
Shawn Rynearson
@srynobio
Jul 14 2017 21:20
Great thanks @mes5k, i'll test this out now!
It a directive as well, which is extra nice, as now I can set it via the config file. Great work guys.