1 go to workflow crispr pipeline main nf add `include FASTQ nf-core #boston-2026-crispr-pipeline

1. go to workflow/crispr_pipeline/main.nf: add `i...

chaochao wong

04/29/2026, 8:05 PM

1. go to workflow/crispr_pipeline/main.nf: add

include { FASTQ_SUBSAMPLE        } from '../../subworkflows/local/fastq_subsample'

chaochao wong

04/29/2026, 8:05 PM

2. add a parameter, named:

subsample = false

in your nextflow.config.

chaochao wong

04/29/2026, 8:06 PM

3. add in line 59 in workflow/crispr_pipline/main.nf:

Copy code

if (params.subample) {
        ch_samples = FASTQ_SUBSAMPLE(ch_samples).out.subsample
    }

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