Closed donaldcampbelljr closed 1 year ago
Per discussion, the pipeline manager should use pipestat.report for the following files:
self.pipeline_profile_file = pipeline_filepath(self, suffix="_profile.tsv")
self.pipeline_stats_file = pipeline_filepath(self, filename="stats.tsv")
self.pipeline_figures_file = pipeline_filepath(self, filename="figures.tsv")
self.pipeline_objects_file = pipeline_filepath(self, filename="objects.tsv")
What was originally reported as a single .tsv
files will be reported into a single .yaml
file.
Annotations will be also be deprecated.
Related to: https://github.com/pepkit/pipestat/issues/21
Currently, Pypiper uses function
_safe_write_to_file
to write items to a local file. However, Pypiper should use pipestat.report instead.As a specific example
stats
are written to a stats.tsv file in a table format:Using pipestat.report from within a Pypiper pipeline manager can be used to write stats: