Verify that adapter sequences are correct for podar dataset

[brooksph]

Truseq?

[brooksph]

We should modify the .settings file downloading adapter sequences step to allow for the use of user specified adapter sequences. This can be done by create a config yaml or json (e.g. https://github.com/common-workflow-language/workflows/blob/master/tools/trimmomatic-illumina_clipping.yaml) file in the same manner we will use to allow the user to specify sequences.

[charlesreid1]

Yes, that's very much part of the plan. The file you linked to defines a default parameters dictionary for the read filtering workflow. That means each of the parameters in that dictionary has the default value seen in that file, but each can be overridden by the user, so they can add this to their workflow parameters .json to use a custom adapter at an arbitrary URL:

(this goes in the Snakefile)

config = {
    ...
    'read_filtering' : {
        ...
        'adapter_file' : {
            'MyAdapter.fa' : 'http://example.com/some/fancy/new/adapter/file.fa'
        }
    }
}