Let’s look at our snakemake “trim” rule from earlier:

Here we specified our inputs/outputs and our shell command.

rule trim:
 input:
 ”reads/sample1.fastq”

 output:
 ”trimmed_reads/sample1-trimmed.fastq”

 shell:
 cutadapt -A TCCGGGTS -o {output} {input}

What to Update in Nextflow?

In looking at our HELLO process, what do we need to add? We already have a publishDir, an output, and script, so let’s update those for cutadapt.

process HELLO {
 publishDir "results/" , mode: "copy"
 output:
 path 'hello.txt'

 script:
 """
 echo 'Hello world!' > hello.txt
 """
}

Update for Running Cutadapt

process  CUTADAPT {
 publishDir "results/" , mode: "copy"

 output:
 path 'trimmed.fastq'

 script:
 """
 cutadapt -a AACCGGTT -o trimmed.fastq ~/sample1.fastq
 """
}

workflow {

CUTADAPT()
}

We can keep ‘results’ as our publishDir for this example, but we’ll need to change our output to trimmed.fastq and we’ll change the command for cutadapt with our adapter and our input and output file names. Because Nextflow executes each task in its own work directory, we need to provide the full path. Our workflow just becomes running the CUTADAPT process.

Does this work? Yes, it does. However, note that we are hard-coding everything and this not really flexible and does not really allow us to scale.