A simple nextflow pipeline to generate the sample sheets for the unicycler, nf-core/bacass, nf-core/viralrecon and the plasmIDent pipeline. It can handle all types of assemblies and was tested with Illumina and Nanopore Reads. Current the pipeline run on the local maschine and require an installation of python (v3.6).
--pipeline to specify one of the above mentioned pipelines
--reads to specify the assembly type by the corresponding reads. You can selcet short, long or hybrid
--mapping_file specfy the file names for the corresponding reads. Default for Nanopore reads is barcode
For short- and long-read assemblies it has to contain a single column with the respectiv name for the short and long read samples.
For the hybrid assembly it contain two tab-separated columns, were the first include all short-read and the second all long-read sample names.
For more information about the pipeline parameter run:
nextflow run jenmuell/nxf-bacass_samplesheet_generator --help