2
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How should I do:

...
if ($(params.aligner) == "bowtie") {
    align_bowtie2(get_fq_info.out.fq_info)
}
else {
    align_bwa(get_fq_info.out.fq_info)
}
...
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1
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You can move that into your workflow definition. There's an example in the docs of how best to use workflow parameters:

A workflow component can access any variable and parameter defined in the outer scope:

params.data = '/some/data/file'

workflow my_pipeline {
    if( params.data )
        bar(params.data)
    else
        bar(foo()) }

Your example workflow would look like:

workflow {

    fq_info = get_fq_info.out.fq_info

    if( params.aligner == "bowtie" ) {
        align_bowtie2( fq_info )
    }
    else {
        align_bwa( fq_info )
    }

    ...
}
```
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1
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Is this inside the main.nf file or inside the process.nf file? Anyway, the param.anything variable should already be available in the nextflow context when executed, thus, you could simply do:

if (params.aligner == "bowtie") {
    align_bowtie2(get_fq_info.out.fq_info)
} else {
    align_bwa(get_fq_info.out.fq_info)
}

Check out this main.nf of a nextflow pipeline of mine, it contains some working if/else snippets.

Here it is another StackOverflow question on conditional nextflow pipelines that might help.

Hope it helps.

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