subsample_table
on a Project
gives the table of sample subannotation / "units" if applicable.attribute
parameter to fetch_samples
function to enable more general applicability.
Additionally, the attribute value matching is more strict now -- requires perfect match.attmap
for implementation of attribute-style access into a key-value collection.sample_annotation
and sample_subannotation
in favor of sample_table
and subsample_table
, respectively.activate_subproject
method to Project
.Project
construction no longer requires sample annotations sheet.implied_attributes
is deprecated.implied_columns
and derived_columns
are deprecated in favor of implied_attributes
and derived_attributes
. numexpr
versions.infer_name
function, which uses a priority lookup to infer the project name: First, the name
attribute in the yaml
file; otherwise, the containing folder unless it is metadata
, in which case, it's the parent of that folder.get_sample
and get_samples
functions to Project
objects.get_subsamples
and get_subsample
functions to both Project
and Sample
objects.subsample_name
as the index column header.peppy
package is now standalonelooper
can now rely on peppy
merge_table
renamed to sample_subannotation
pep
)--dry-run
.pipeline_args
section.--lump
and --lumpn
options--include-protocols
pipeline_interface.yaml
files, increasing flexibility, so this relaxes the specified folder structure that was previously used for pipelines_dir
(with config
subfolder).pipelines_dir
to pipeline_interfaces
(but maintained backwards compatibility for now).run
column to toggle
, since run
can also refer to a sequencing run.setuptools
for installation, and pandas 0.20.2
. If numexpr
is installed, version 2.6.2
is required.pipeline_interfaces
--version
and -V
options and printing version at runtimeall_input_files
and required_input_files
attributeslooper summarize
) replacing the summarizePipelineStats.R
scriptlooper check
) replacing the flagCheck.sh
scriptlooper destroy
) to remove all output of a projectlooper clean
) to remove intermediate files of a project flagged for deletionpipelines
repository installed in order to extend base Sample objects