channel From Path returns null even though file exists

[zillurbmb51]

Hi,
I wanted to create a channel with certain file as below:

nextflow.enable.dsl=1
channel.FromPath('/cluster/projects/p33/users/gledak/metabolomics/lipids/out/*_permuted*.glm.linear').view()

But it gives me error:
Cannot invoke method view() on null object

Any help? Attached is the log.
nextflow.log3.txt

[manuelesimi]

You get a null object because you are invoking a method that does not exist.

It should be:
channel.fromPath('...').view()
Do note the lowercase f in fromPath.

[mribeirodantas]

The first letter in Channel must be uppercase, and the first letter in the channel factory fromPath must be lowercase 😃

Check below for the right syntax (The indentation, spacing, is optional but makes it easier to read so I'm going to use it here):

Channel
  .fromPath('/cluster/projects/p33/users/gledak/metabolomics/lipids/out/*_permuted*.glm.linear')
  .view()

It's also important to mention that DSL1 has been deprecated and is no longer supported in recent versions of Nextflow. You should use DSL2 instead.

[manuelesimi]

channel is an alias of Channel since version 20.07.0 (see https://www.nextflow.io/docs/latest/channel.html#channel-factory), so it should work.

Agree that DSL1 should be avoided as much as possible.

[mribeirodantas]

Thanks for pointing this out, @manuelesimi. I completely forgot about it 😓

[nick-youngblut]

I've developed many Nextflow pipelines, and for starting a new pipeline, I'm stuck on this simple aspect:

myFileChannel = Channel.fromPath( '/data/some/bigfile.txt', checkIfExists = true )
println( myFileChannel )

...returns null, and there is no check on whether the file exists.

I'm using Nextflow v24.04.4. What is going on???

[nick-youngblut]

It all came down to checkIfExists = true instead of checkIfExists: true. The misleading (or lacking) error messages in Nextflow can waste so much time.

[nick-youngblut]

Maybe this a groovy-level issue, but Channel.fromPath( '/data/some/bigfile.txt', checkIfExists = true ) should really throw an error instead of returning null.

[bentsherman]

It will soon. Stay tuned 😄