looper table appears to re-create the item once per sample, and makes empty table

[nsheff]

Not sure if this is actually a problem in the code, or just in the messaging, but this messages don't make sense when you run 'looper table':

> looper table
looper table
Looper version: 2.0.0a2
Command: table
Using looper config (.looper.yaml).
No config key in Project, or reading project from dict
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline/PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline/PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline/PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline/PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline/PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
Creating objects summary
'PEPATAC' pipeline stats summary (n=1): /project/shefflab/brickyard/results_pipeline//PEPATAC_stats_summary.tsv
'PEPATAC' pipeline objects summary (n=0): /project/shefflab/brickyard/results_pipeline//PEPATAC_objs_summary.yaml
...

[nsheff]

Also, the final PEPATAC_stats_summary.tsv file is actually empty:

cat PEPATAC_stats_summary.tsv
Sample Index	Record Identifier	Pipeline Type

[nsheff]

So this is really 2 issues in one. The second issue is probably related to #537 (same problem in both looper table and looper report)

[donaldcampbelljr]

This is probably related to #522