This work makes the pipeline more versatile. The wrapper python script is now able to handle any bpipe pipeline (although some options are still expected). I have separated initial fastq processing from variant calling. It is possible to run the same variant calling pipeline we have always done ( now in two steps). We can also add any other variant calling software. I have provided a simple script that counts the bases at each position. The pipeline also now comes with with a conda environment to handle python dependencies (outside of flux) and a R packrat file to handle dependencies in R (for the deepSNV pipeline). This should address issues with the tutorial as well.
This work makes the pipeline more versatile. The wrapper python script is now able to handle any bpipe pipeline (although some options are still expected). I have separated initial fastq processing from variant calling. It is possible to run the same variant calling pipeline we have always done ( now in two steps). We can also add any other variant calling software. I have provided a simple script that counts the bases at each position. The pipeline also now comes with with a conda environment to handle python dependencies (outside of flux) and a R packrat file to handle dependencies in R (for the deepSNV pipeline). This should address issues with the tutorial as well.