path output into FromPath

[RamilNurtdinov]

Hi

I use DSL2
nextflow.enable.dsl=2

I have a process that makes a file and return it as path variable

output:
        path "Expressed.genes.tsv"

I want to read this file with FromPath

    channel
        .fromPath(file(genes_index))
        .splitCsv(header:true, sep: '\t')

I got error:
class groovyx.gpars.dataflow.expression.DataflowInvocationExpression cannot be cast to class java.nio.file.FileSystem (groovyx.gpars.dataflow.expression.DataflowInvocationExpression is in unnamed module of loader 'app'; java.nio.file.FileSystem is in module java.base of loader 'bootstrap'

Eventually I need to emit a channel with every line from the "path" object.

Be grateful if somebody can help me with it.

Ramil
.

[pditommaso]

I guess genes_index is already a channel therefore you don't need (and can't) to use channel.fromPath. Try instead

genes_index.splitCsv(header:true, sep: '\t')

[RamilNurtdinov]

Thank you Paolo
This works.

I am running the following command:
expressed_genes = Expressed_genes(data_folder,tissues,chunks,s_status) | splitCsv(header:true, sep: '\t') | toList()
The Expressed_genes process returns output: path "Expressed.genes.tsv" and the content of this file is redirected to splitCsv somehow.

From my point of view you need to update the manual.
Either the path variable can be simultaneously the content of its file, or splitCsv understands the path variable and reads corresponding file.