Rules are documented and we developed a Sphinx extension to automatically add their docstring in this documentation. For example, the documentation of the rule fastq_sampling looks like:
A sample from raw FastQ files
- Required input:
- __fastq_sampling__input_fastq: list of fastq.gz files
- Required output:
- __fastq_sampling__output_fastq: list of fastq.gz files
- Required configuration:
- fastq_sampling: N: # number of reads to select
Uses sequana_fastq_head utility.
In order to use a Sequana rule in your pipeline, add this code:
from sequana import snaketools as sm include: sm.modules["fastq_sampling"]
This takes care of the physical location of the rule. Of course, you will then need to look at the documentation and define the required variables in your pipeline. For instance, in the example above, given the documentation, you will need to define those two variables:
and have a configuration file with:
fastq_sampling: N: 1000
Many rules are used inside the Sequana pipelines but not all. For instance, the codecs rules (e.g. gz_to_bzip) are used in standalones.
Please see the Pipelines section for other rule documentation (e.g. bwa, fastqc, …).