Defines paths for both local and remote binaries and databases. A template is provided in the examples directory.
.. literalinclude:: ../../examples/parameters.yaml
Defines the steps that the pipeline will execute. A template is provided in the /examples directory.
Step names correspond to a python module that will launch the step. Step names are split based on the '_' character so you can launch multiple instance. For example you might want to launch blastx and blastn, so step names could be 'Blast_N' and 'Blast_X'. What is after the underscore do not matters, it is just used to differanciate the two steps.
Special words in bracket are used as substitution string. - (file), (file1) and (file2) - (SampleID) - (library)
.. literalinclude:: ../../examples/step.yaml
The map file describe the experiment. It is a tabulated file with the first line containing headers starting with '#'. It must contain at least two column: SampleID and file.
A template is provided in the examples directory.
This is a minimum map.txt file:
.. literalinclude:: ../../examples/map.txt
You can add categories for each sample so they can be used when coloring sequences in trees from the Rps2tree module. One library can be attributed to multiple samples, as shown in the example. Thus the demultiplexing step will be able to differentiate each sample and separate them.