assembly tool as input parameter

[grendon]

Something like params.asssemblytool. The value could be megahit or masurca.

You should create an assembly process for each tool and then make the execution of the assembly process conditional on the value of that parameter.

If tool=megahit then execute process assemblyMegahit.
If tool=masurca then execute process assemblyMasurca.

There are several examples of conditional processes. This snippet is in nextflow templates;

https://github.com/nextflow-io/patterns/blob/master/docs/conditional-process.adoc

[grendon]

done

[kkowalden]

@grendon When a config file with assembler="masurca" is used with pipeline, both megahit and masurca run.
Probably needs an if/else statement.

[cjfields]

Still runs with both with the overhauled code, so should probably be addressed with masurca as the default.