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.
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
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