Running Slinker is as simple as setting up some initial parameters and then executing a command in the terminal. The bpipe pipeline will do the rest.

Each of these parameters need a value assigned:

• case=<path/to/case/.bam>
  The case_sample parameter tells the pipeline that a particular sample is of interest. Basically, this parameter can be any string that is included in the sample path.

• gene=<gene_name>
  A gene name using the HUGO naming conventions. I.e. IKZF1 or BCR or ABL1.

• genome=38 or genome=19
  Hopefully self explanatory. What reference are your input samples aligned to?

• results=/path/to/output/
  Where do you want the results saved?

• threads=4
  Set the number of threads open to the pipeline.

• samples=$(ls $PWD/*.bam) in a folder with only the control bam files or
  samples="/path/to/sample1_Aligned.sortedByCoord.out.bam /path/to/sample2_Aligned.sortedByCoord.out.bam
  
  Pass the samples, including paths, into a variable. These can be simlinks in a folder or you can just manually add each.

You've done the heavy lifting. Hopefully you can figure out better internal processes that will speed that up for you. But not just simply run the below snippet and you will start getting results.

bpipe -p case_sample=$case -p gene=$gene -p genome=$genome -p a_mem=20000000000 -p g_mem=20000000000 -p results=$results -p threads=$threads $SLINKERDIR/workflows/slinker.groovy $samples $case