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  • 01:31
    nttg8100 opened #3449
  • Nov 29 19:15

    pditommaso on master

    Remove dsl1 output mode Signed… (compare)

  • Nov 29 18:11

    pditommaso on master

    Fix tower plugin min nextflow r… Bump nf-tower@1.5.7 Signed-off… Bump nf-wave@0.6.1 Signed-off-… and 2 more (compare)

  • Nov 29 17:50
    pditommaso commented #2392
  • Nov 29 17:49
    pditommaso closed #2412
  • Nov 29 17:49
    pditommaso commented #2412
  • Nov 29 17:47
    pditommaso closed #2333
  • Nov 29 17:47
    pditommaso commented #2333
  • Nov 29 17:45
    pditommaso closed #1843
  • Nov 29 17:45
    pditommaso commented #1843
  • Nov 29 17:43
    pditommaso closed #1266
  • Nov 29 17:43
    pditommaso commented #1266
  • Nov 29 17:42
    pditommaso closed #2460
  • Nov 29 17:42
    pditommaso commented #2460
  • Nov 29 17:40
    pditommaso closed #2999
  • Nov 29 17:40
    pditommaso commented #2999
  • Nov 29 16:42

    pditommaso on v22.11.1-edge

    (compare)

  • Nov 29 15:31
    bentsherman labeled #3443
  • Nov 29 15:25

    pditommaso on edge-22.11.x

    Fix TowerArchiver resolve envar… Update changelog Signed-off-by… [release 22.11.1-edge] Update t… (compare)

  • Nov 29 15:19
    bentsherman commented #2893
Alaa Badredine
@AlaaBadredine_twitter
you can directly call your perl script within the script block of nextflow. So, you actually don't have to write perl code inside Nextflow, just give the path of your script and gives the right output and input and it should work
banjosnapper
@banjosnapper
@AlaaBadredine_twitter I get an error saying that my script.pl does not exist. Should I be putting my script in a particular place to be able to call it? It is within the same directory as the main.nf
Alaa Badredine
@AlaaBadredine_twitter
what's your script name ?
banjosnapper
@banjosnapper
I called it 'parseme.pl'
Alaa Badredine
@AlaaBadredine_twitter
replace script.pl by your actual script name
banjosnapper
@banjosnapper
That is what I did do
Alaa Badredine
@AlaaBadredine_twitter
ok so it would be perl /path/to/your/script/perseme.pl
you have to give the full path of your script
you can define it as a variable
banjosnapper
@banjosnapper
Okay I will try and give it the full path
Alaa Badredine
@AlaaBadredine_twitter
somewhere in nextflow
parseme = "/full/path/to/parseme.pl"
and then call it: perl $parseme
banjosnapper
@banjosnapper
Thank you that worked. However, I am still getting exir error status 2 when executing
Caused by:
  Process `swapID` terminated with an error exit status (2)

Command executed:

  perl /scratch/c.c1860369/nextFlow/bin/parseme.pl

Command exit status:
  2

Command output:
  (empty)

Command error:
  Died at /scratch/c.c1860369/nextFlow/bin/parseme.pl line 10.
banjosnapper
@banjosnapper
Okay so I worked out the isse. It was because I did not give an absolute path name to the mmuChr.gff3 in the perl script. Many thank for your help @AlaaBadredine_twitter
Alaa Badredine
@AlaaBadredine_twitter
@banjosnapper no problem
mmatthews06
@mmatthews06
@pditommaso or anyone else, did anybody catch my question about attaching a debugger to Nextflow? Or running Nextflow in IntelliJ in debug mode, to set breakpoints, etc.? I'm starting back working on that, just thought I'd ask for any quick hints, since I assume somebody has already done it.
Paolo Di Tommaso
@pditommaso
it's possible for the nextflow runtime development, but I guess you want for nextflow scripts
mmatthews06
@mmatthews06
No, runtime development. I'm mucking around Nextflow internals for the time being.
Paolo Di Tommaso
@pditommaso
then it's straightforward, use ./launch.sh -remote-debug run .. etc
mmatthews06
@mmatthews06
Ah, alright, I'll try that. Thanks!
Paolo Di Tommaso
@pditommaso
Workflow components in the pipeline :sunglasses:
Stephen Kelly
@stevekm
@banjosnapper put your scripts in a directory called bin adjacent to the main nextflow script; example here: https://github.com/stevekm/nextflow-demos/tree/1238d0c444f388cb1ee79c351a57610e03e4bbb6/R-Python
as long as the scripts are executable then you can just invoke them directly from within your task
Guillaume Theaud
@GuillaumeTh
@pditommaso I saw that now in the .command.run the values for the environment variable are written like MY_VAR=\"0\" whereas in the 19.04 the variable was MY_VAR="0". This modification is normal ?
Stephen Kelly
@stevekm

@banjosnapper instead of calling your script with perl myscript.pl you should instead put a shebang at the very first line that invokes the perl interpreter, see this Python script that includes one: https://github.com/stevekm/nextflow-demos/blob/1238d0c444f388cb1ee79c351a57610e03e4bbb6/R-Python/bin/test.py

this allows you to invoke the script as simply myscript.pl

Paolo Di Tommaso
@pditommaso
@GuillaumeTh :point_right: nextflow-io/nextflow#1146
Guillaume Theaud
@GuillaumeTh
@pditommaso thanks
@pditommaso The problem that I have in my case is that in the config file I set env {NB_PROCESSES=1} But with the fix the value of NB_PROCESSES="1" but some scripts requiered a int not a string. Do you have a idea to set a int instead of a string in the nextflow.config ?
Paolo Di Tommaso
@pditommaso
Don't think env vars distinguish between num and string
Stephen Kelly
@stevekm

sometimes when I restart a Nexflow pipeline with -resume, I get errors inside my processes such as java.lang.NullPointerException: Cannot get property 'outputDir' on null object. These come from processes that look like this:

process vcf_to_tsv {
    publishDir "${params.outputDir}/VEP/vcf_tsv", mode: 'copy'
    // stuff
}

so it seems like params is not always getting initialized correctly when the pipeline resumes.

I have the same error for dict objects that I initialize from reading in a JSON. Sometimes, the pipeline errors out when I try to access the object's keys inside a process. Problem is, all of these errors are completely random and not reproducible. Eventually if I restart the pipeline enough times with -resume, they go away. Or not, and I just start the pipeline from scratch... is this a known bug? I think we are still using 19.01

here is one such stack trace:
Dec-18 09:01:45.818 [PathVisitor-1] ERROR nextflow.Channel - Cannot get property 'outputDir' on null object
java.lang.NullPointerException: Cannot get property 'outputDir' on null object
        at org.codehaus.groovy.runtime.NullObject.getProperty(NullObject.java:60)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190)
        at org.codehaus.groovy.runtime.callsite.NullCallSite.getProperty(NullCallSite.java:46)
        at org.codehaus.groovy.runtime.callsite.GetEffectivePogoPropertySite.callGetProperty(GetEffectivePogoPropertySite.java:45)
        at _nf_script_121eedc3$_run_closure117$_closure442.doCall(_nf_script_121eedc3:2192)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
        at groovy.lang.Closure.call(Closure.java:411)
        at groovy.lang.Closure.call(Closure.java:405)
        at groovy.lang.GString.writeTo(GString.java:189)
        at groovy.lang.GString.toString(GString.java:153)
        at org.codehaus.groovy.runtime.typehandling.ShortTypeHandling.castToString(ShortTypeHandling.java:55)
        at nextflow.extension.Bolts.asType(Bolts.groovy:474)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:54)
        at org.codehaus.groovy.runtime.metaclass.NewInstanceMetaMethod.invoke(NewInstanceMetaMethod.java:56)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1235)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
        ......
Paolo Di Tommaso
@pditommaso
it seems an app issue, outputDir is not a NF variable
Stephen Kelly
@stevekm
It is defined inside the main.nf pipeline;
params.outputDir = "output"

process vcf_to_tsv {
      publishDir "${params.outputDir}/VEP/vcf_tsv", mode: 'copy'
....
....
}
this way the user is able to override it from the CLI
nextflow run main.nf --outputDir foo/
I thought this was standard practice?
Paolo Di Tommaso
@pditommaso
weird, try the latest version, if the problem persits open an issue
Stephen Kelly
@stevekm
ok
what was the arg to disable the ANSI logger in the latest?
Paolo Di Tommaso
@pditommaso
-ansi-log false
Stephen Kelly
@stevekm
oh sorry I meant the environment variable...
Paolo Di Tommaso
@pditommaso
NXF_ANSI_LOG=false
Stephen Kelly
@stevekm
I get a lot of these... WARN: The channel 'create' method is deprecated -- it will be removed in a future release
:(
Ha Le
@haqle314
Yeah, disabling ANSI logger just means that nextflow will print out plain logs without color, '\r', etc. I think nextflow should print warning messages to stderr instead of stdout as it currently does. This way, people that dont want to see the warnings can do nextflow ... 2>/dev/null.
Stijn van Dongen
@micans
Is it possible not to use the time directive? In some cases I'd like to depend on whatever the (LSF) queue maximum is, perhaps in a process-specific manner. This would also avoid the problem that it is a (bsub) error to specify a time limit larger than the queue limit. And can this be done also using override, so e.g. default might be 12.h but for some process I want to turn it off.
Adrian Viehweger
@phiweger
using DSL2, how can I specify that a process uses 2 channels as input, when one channel only contains 1 item, ie channel A has "asm = [s1, s2]" and channel B has "db = [db]" and I want to perform some process with [s1, db] and [s2, db]. I tried foo(asm, db) but this starts only [s1, db] and ignores [s2, db].
Steve Frenk
@sfrenk
@phiweger Are you sure that s1 and s2 are being emitted separately rather than as a single list? eg. you may need to use flatten() or flatMap()
Has anyone had experience using Spock or JUnit (or other unit testing framework) with DSL2? I'm trying to figure out a way of getting the Specification class to have access to processes and channels.
Krittin Phornsiricharoenphant
@sinonkt
@pditommaso Just want you guys know that DSL2 is really awesome, That helps a lot Thank you so much!