Snakemake 6.2

New Feature:

Integration with other workflow management systems, e.g. Nextflow

Handover rules

rule chipseq_pipeline:
    input:
        input="design.csv",
        fasta="data/genome.fasta",
        gtf="data/genome.gtf",
    output:
        "multiqc/broadPeaks/multiqc_report.html",
    params:
        pipeline="nf-core/chipseq",
        revision="1.2.1",
        profile=["conda"],
    handover: True
    wrapper:
        "0.74.0/utils/nextflow"

declare rules that hand over resources to other WMS

  • all resources are passed to the rule
  • the foreign system can be configured to submit to the same cluster or cloud
rule chipseq_pipeline:
    input:
        input="design.csv",
        fasta="data/genome.fasta",
        gtf="data/genome.gtf",
    output:
        "results/multiqc/broadPeaks/multiqc_report.html",
        directory("results/bwa/mergedLibrary/bigWig"),
    params:
        pipeline="nf-core/chipseq",
        revision="1.2.1",
        profile=["conda"],
    handover: True
    wrapper:
        "0.74.0/utils/nextflow"


rule plot_something:
    input:
    	"results/bwa/mergedLibrary/bigWig"
    output:
    	"results/plots/something.pdf"
    conda:
        "envs/pystats.yaml"
    notebook:
        "notebooks/plot-something.py.ipynb"

Example application

Snakemake 6.2

By Johannes Köster

Snakemake 6.2

New features in Snakemake 6.2

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