johanneskoester

conf = ... # load the config file here


########### some helper functions to aggregate input files ##########


def prefix2samples(wildcards):
    # retreive the treatment or control samples for the given prefix here
    return expand("{sample}.bam", sample=...)

johanneskoester

settings:
   default:
       cufflinks: "--param1=20 ..."
   other:
       cufflinks: "--param1=15 ..."

johanneskoester

johanneskoester

Keybase proof

I hereby claim:

• I am johanneskoester on github.
• I am johanneskoester (https://keybase.io/johanneskoester) on keybase.
• I have a public key ASBb4dzF5tXeo5pEdc9AHaGs9GITSHiltvp7FmnSTd_OKAo

To claim this, I am signing this object:

johanneskoester

filetypes:
  # this directive automatically generates flags for each type that can be used in the rules below
  fq="edam:format_1929"
  fa="edam:format_1930"
  bam="edam:format_2572"

rule bwa:
    input:
        fq("genome.fa"),