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yanhui09 / laca

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
GNU General Public License v3.0
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Provide additional customisation options during init step for generation of the config file #2

Open ahfitzpa opened 1 year ago

ahfitzpa commented 1 year ago

I would like to use LACA for shorter amplicons (600 bp) from ONT sequencing.

Can you provide the following options in the laca init so that the config file can work with alternative sequence input?

yanhui09 commented 1 year ago

Thanks for interesting in LACA. laca init is actually wrapped cmd to generate the snakemake config.yaml. There are many variables in config file, so at this moment I only include as commonly used ones as cmd arguments. Like fw_primer or rev_primer, some users may have multiple sets, so it's a bit hard to be integrated in the arguments. But any time you can edit the config.yaml file which is generated by laca init.

I have referenced to lines to adjust primers and amplicon length

amplicon length: https://github.com/yanhui09/laca/blob/2af0f0e59f4a250146da6589f1715e5853340792/laca/workflow/config_template.yaml#L38-L39

fw/rev_primer: https://github.com/yanhui09/laca/blob/2af0f0e59f4a250146da6589f1715e5853340792/laca/workflow/config_template.yaml#L44-L51