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"- use nf-core workflow
- extend it with additional plots for your paper, e.g. via Snakemake's notebook integration
Example application
Snakemake 6.2
By Johannes Köster
Snakemake 6.2
New features in Snakemake 6.2
