CODEWITHSUNDEEP
bioinformaticspipelinenextflow
xihh
xihh

Reputation: 309

How to combine multiple queue channels with values in Nextflow?

I want to run an analysis multiple times with different variables on the same input from a previous processes on Nextflow:

process a {
    output:
    file id, "{id}.out" into a
}

metadata = Channel.fromPath("metadata.tsv")

vars_to_analyze = Channel.from(["var_a", "var_b"])

process b {
    input:
    tuple id, file from a
    file m from metadata
    val var from vars_to_analyze

    output:
    tuple id, path("${id}-${var}.out") into b

    """
    command --var ${var} --metadata ${m} ${file} > ${id}-${var}.out
    """
}

Which is the correct way to re-use metadata and file with different values?

Upvotes: 1

Views: 1557

Answers (1)

pditommaso
pditommaso

Reputation: 3381

Don't use a channel for the metadata file, just declare as

metadata = file("metadata.tsv")

Upvotes: 2

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