Merging from issue 15 (multi-sample possibility) #23
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Docker runOptions to specify "--platform linux/amd64"
The substitution is properly working! Now, to create a release of the data I must test all the assembly options, again.
Changing this instead of default as a suggestion so users can use it with the --unicycler_additional_parameters parameter.
Making module call more generic
Tested only in nanopore only assembly
Tested only in nanopore only assembly workflow
Adding wtdbg2 and shasta to hybrid assemblies where long reads assemblies are polished with short reads
* params given via .config or cli are used as defaults for all samples * if a sample has one of these configurations in the YAML, it will overwrite the defaults and work as the major rule for that specific sample
* removing the "long reads type" checking that was performed inside the module * it will use directly the value given from the .config/cli or YAML
adding parameter check on "corrected_long_reads" key
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This pull request has the new implementation of the pipeline, which, by taking advantage of a YAML samplesheet as input makes it cleaner and straightforward to perform the analysis seamlessly with one or multiple samples at once.
It has a major change, and, therefore, triggers a new major release, v3.0