Running Pipeline after Local install

[whottel]

Hello,

Besides singularity, I also tried the local installation option.

The download completed and I was able to run runVarpipeline.sh after copying my paired gzipped fastq files in the data/ directroy.
The pipeline ran to completion without printing an error messages to the terminal, but looking into the output files I noticed that most of the created files were empty, although the Lineage and interpretation file seemed to be generated correctly.
Looking at the Nextflow log I see

Command error:
  .command.sh: line 2: clockwork: command not found

I still see this error after updating the tools/clockwork-0.11.3/clockwork script to point at the full path to the clockwork image.

-Wes