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baffoloco
baffoloco

Reputation: 25

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

Upvotes: 1

Views: 2013

Answers (2)

ybendana
ybendana

Reputation: 1643

I was looking into getting the value from a channel and was getting DataFlowVariable(null) when trying to print out the stdout channel although when I used view I could see the value. I then looked at the api doc for DataFlowVariable and realized that the then function can wait for the value to be set in the asynchronous channel.

I didn't see this mentioned in the Nextflow docs so this is probably not a best practice but could be useful in certain situations.

process output_json {
    output:
    stdout

    script:
    """
    echo '{"a": true}'
    """
}

workflow {
    json = output_json | collect
    json.then { print json.val[0] }
}

Upvotes: 0

Steve
Steve

Reputation: 54502

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

Upvotes: 2

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