Note
Go to the end to download the full example code.
5.6. Pipeline statistics
First, let us get the data
from sequana_pipetools.snaketools import get_pipeline_statistics
stats = get_pipeline_statistics()
{'coverage': 3, 'demultiplex': 9, 'denovo': 24, 'fastqc': 8, 'mapper': 21, 'quality_control': 9, 'rnaseq': 33, 'variant_calling': 25}
Plot number of rules per pipeline
Note that pacbio_qc is self-content
Proportions of rules re-used
Amongst the rules, about a third of the rules are not used at all in the pipelines. There are two reasons: either they were part of previous pipeline versions and were discarded in favour of new tools, or there were used for testing and kept in case of.
Then, we can see that a third of the rules are used only once. And finally, about a third used more than once.
([<matplotlib.patches.Wedge object at 0x7f7839028eb0>, <matplotlib.patches.Wedge object at 0x7f78392683a0>, <matplotlib.patches.Wedge object at 0x7f783902b9d0>, <matplotlib.patches.Wedge object at 0x7f783902b670>, <matplotlib.patches.Wedge object at 0x7f783902ace0>], [Text(0.834633933216614, 0.7165097330276574, '7 used 2 times'), Text(-0.055714017004277645, 1.098588161373154, '2 used 5 times'), Text(-1.0108535099305853, -0.43379163369181745, '17 used 1 times'), Text(0.8346342720316069, -0.7165093383552442, '3 used 3 times'), Text(1.077483068211768, -0.2214277257186978, '2 used 6 times')])
Total running time of the script: (0 minutes 0.223 seconds)