Config file (snake.scatter.yaml) not present

[tybottorff]

Describe the bug
mgatk call stops due to issues with config files, doesn't produce output files. I'm guessing that lines like these Workflow defines configfile ../mgatk_output/.internal/parseltongue/snake.scatter.yaml but it is not present or accessible (full checked path: /path/to/mgatk_output/.internal/parseltongue/snake.scatter.yaml). are central to the issue here, thus the title. That config file is not present (no .internal dir)

To Reproduce
My script is...

#!/bin/bash
source venv3/bin/activate
mgatk call -i ../raw_data/combined_bams/ -g GRCh38 -o ../mgatk_output
deactivate

The combined_bams dir has .bam files from bulk ATACseq experiment that had ~10-20% MT reads across libraries (each 1 .bam file here).

Attached file has more output log info
log.md

When running mgatk call on the test data (i.e. mgatk call -i git/mgatk/tests/humanbam/ -g hg19 -o ../mgatk_output), I get very similar errors

[caleblareau]

this was an issue with how call was being processed, which should be addressed with the latest commit if you want to try?