groovybioinformaticsnextflow

Converting Channels into strings in Nextflow DSL2


I'm wondering how to extract the content of a Nextflow Channel and make it a string, within the workflow block.

I'd need this for example to:

I already tried .toString(), .map{}, .view() and everything I could find in the documentation


Solution

  • I'm wondering how to extract the content of a Nextflow Channel and make it a string

    Best to avoid trying to do this. If you just want to select a map key based on a process' output, you can simply declare your map in your workflow block and use it as required. For example:

    process test {
    
        input:
        val myval
    
        output:
        path "${myval}.txt"
    
        """
        touch "${myval}.txt"
        """
    }
    
    workflow {
    
        def foobarbaz = ['foo': 1, 'bar': 2, 'baz': 3]
    
        Channel.of('foo', 'bar', 'baz')
            | test
            | map { tuple( foobarbaz[ it.baseName ], it ) }
            | view()
    }
    

    Results:

    $ nextflow run main.nf 
    N E X T F L O W  ~  version 22.10.0
    Launching `main.nf` [high_faggin] DSL2 - revision: 43aaa56eee
    executor >  local (3)
    [0e/0fd6dc] process > test (3) [100%] 3 of 3 ✔
    [1, /path/to/work/a7/d501cb2a8426c5639117d14e8fb7fe/foo.txt]
    [2, /path/to/work/22/df9cc4f1d34b9cca0d0331fac5c150/bar.txt]
    [3, /path/to/work/0e/0fd6dc0519a34c52903b990755f450/baz.txt]
    

    Note that you do not need the watchPath factory method to watch the output path of a previous process. Simply define the previous process' outputs in the output block and declare them as inputs in the downstream process' input block. For example:

    process foo {
    
        input:
        val myval
    
        output:
        path "${myval}.txt"
    
        """
        echo "value: ${myval}" > "${myval}.txt"
        """
    }
    
    process bar {
    
        input:
        path myfile
    
        output:
        stdout
    
        """
        echo "Contents of ${myfile}:" 
        cat "${myfile}"
        """
    }
    
    workflow {
    
        Channel.of('foo', 'bar', 'baz')
            | foo 
            | bar
            | view()
    }
    

    Results:

    $ nextflow run main.nf 
    N E X T F L O W  ~  version 22.10.0
    Launching `main.nf` [clever_lovelace] DSL2 - revision: c388bd26af
    executor >  local (6)
    [ac/1be228] process > foo (2) [100%] 3 of 3 ✔
    [11/7b3c6e] process > bar (1) [100%] 3 of 3 ✔
    Contents of foo.txt:
    value: foo
    
    Contents of bar.txt:
    value: bar
    
    Contents of baz.txt:
    value: baz