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johanneskoester / snakemake_macs.py
Last active December 29, 2015 00:19
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
johanneskoester / gist:9212320a8aa2a24b18f500b424c22eb4
Created August 17, 2016 15:06
settings:
default:
cufflinks: "--param1=20 ..."
other:
cufflinks: "--param1=15 ..."
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johanneskoester / chrM.cancer.bam
Last active April 11, 2017 12:43
Example data for nygenome/lancet#4
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johanneskoester / keybase.md
Created November 16, 2017 06:59

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
johanneskoester / snakemake-types
Last active July 7, 2019 12:02
One way to possibly include type annotations to Snakemake workflow definitions. One could for example use ontologies like edam, as well as mime types.
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"),