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Johannes Köster johanneskoester

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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.
View snakemake-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"),
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View gist:9212320a8aa2a24b18f500b424c22eb4
settings:
default:
cufflinks: "--param1=20 ..."
other:
cufflinks: "--param1=15 ..."
View snakemake_macs.py
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=...)