On methylseq pipeline, how to specify a different library length for bismark?

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1

We are trying to fine-tune the pipeline to analyze samples that were sequenced with the Pico methylseq library prep kit. Especially the methylation consisntency results.

We want to try adding the bismark option for specifying a different library size.
We already tried adding it at the command line as an additional parameter

nextflow run nf-core/methylseq -r 2.6.0 ... --bismark_options "--length 1500"

But it was completely ignored as shown below:

Oct-15 12:45:52.448 [main] WARN nextflow.validation.SchemaValidator - The following invalid input values have been detected:

  • –bismark_options: --length 1500

Is there a way to include that parameter?

Thanks in advance for your help.

2

You should be able to provide bismark options by using the task.ext.args in a configuration file.

Check here in the nf-core docs for more info and an example. Something like:

  process {
    withName: bismark_align {
        ext.args = {
          [                                           // Assign a closure which returns a string
            '--length 1500',
            '--other-options example',
          ].join(' ')
        }                                                // Join converts the list here to a string.
        ext.prefix = { "${meta.id}" }    // A closure can be used to access variables defined in the script
    }
  }
3

Great. I will give it a try. Thanks a lot!

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