update module: CHOPPER

[muabnezor]

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[muabnezor]

chopper can be used together with a fasta file to filter reads against. The current module does not allow for the user to pass along a fasta file as an input. However, chopper can also be used without a fasta file for quality, and length filtering, so the option to pass along a fasta file must be flexible.

[muabnezor]

Hi, what would be the best way of doing this? We want to be able to use chopper with, and without a reference fasta to filter against. I'm inclined to let the fasta file to be an optional parameter, but it seems there is no straightforward way to give optional parameters in nextflow? would it be better to add an additional chopper module, e.g. chopper_reference, that takes an fasta file as input as well? What do you think @jfy133

[jfy133]

@muabnezor optional inputs are possible! Pseudocode

script:
def fasta_command =  fasta ? '-contam ${fasta}' : ''
"""
chopper -i ${fastq} $fastq_command
"""

[jfy133]

For the module invocatroin you can use an empty list [] e.g. CHOPPER ( ch_fastaqs, [] ) if you don't have a fasta

[muabnezor]

Great,

I did it like that, but I had problems with the invocation when the fasta channel is empty. passing [] seems to do it.

So chopper can be invoked with something like this

            CHOPPER (
                ch_long_reads,
                lambda.ifEmpty([])
            )

PR in nf-core/modules coming soon.

[jfy133]

Exactly!