Donald Campbell

Related to https://github.com/pepkit/looper/issues/484 Currently, if no name is given in the project config, the project name is simply inferred as 'project'. However, no such thing occurs for PEPs loaded from...

Should appending sample modifiers override column values in sample.csv?

1

I noticed that appending a value via sample modifiers in the project config will not override a column value if it already exists in the sample.csv table, e.g. ``` name:...

Discovered this recently as I was refactoring Looper tests; the naming of this constant is inaccurate: 

Using v0.40.0 can create peppy project without sample names.

1

Example: ``` sample_name,library,file,toggle ,anySampleType,data/frog1_data.txt,1 frog_2,anySampleType,data/frog2_data.txt,1 ``` Can create peppy prj with missing sample name. ``` sample_name: None library: anySampleType file: data/frog1_data.txt toggle: 1, Sample 'frog_2' in Project (/home/drc/GITHUB/hello_looper/hello_looper/project/project_config.yaml) sample_name: frog_2...

multi=False causes Errno 29 illegal seek during pytest teardown

4

Reproduce by setting the multi flag to false or just leaving it out: ``` def test_temp_test(): pp = pypiper.PipelineManager( "sample_pipeline", outfolder="/home/drc/Downloads/BED_CLASSIFIER_OUTPUT/", multi=True ) ``` If you set the flag `multi=True`,...

report_result docstrings for value is inaccurate

2

I am experiencing this as I use pypiper in Bedbase. `pm.report_result(key="bedtype", value=self.bed_type)` It expects value to be a dict, but it does not need to be a dict. It could...

Tests should clean up after running

3

Currently, it appears that tests for pypiper are generating results in a tmp directory that is not being cleaned up once pytesting is finished.