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johanneskoester/gist:9212320a8aa2a24b18f500b424c22eb4

Created August 17, 2016 15:06
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gistfile1.txt
settings:
default:
cufflinks: "--param1=20 ..."
other:
cufflinks: "--param1=15 ..."
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rule cufflinks:
    input: ...
    output:
        "results/{settings}/cufflinks/transcripts.fpkm_tracking"
   params:
        custom=lambda wildcards: config["settings"][wildcards.settings]["cufflinks"]
    shell:
         "cufflinks {params.custom}"

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