Use conditional in workflow in Nextflow dsl2 How should I do:
...
if ($(params.aligner) == &quot;bowtie&quot;) {
    align_bowtie2(get_fq_info.out.fq_info)
}
else {
    align_bwa(get_fq_info.out.fq_info)
}
...
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 == &quot;bowtie&quot;) {
    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.