https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/franciscozorrilla/metaGEM.html

https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/fischuu/Snakebite-Holoruminant-MetaG.html

mamba env create -n metagem -f envs/metaGEM_env.yml

mamba env create –prefix ./envs/metagem -f envs/metaGEM_env.yml

https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/GooglingTheCancerGenome/sv-callers.html

mamba env create -n sv-callers -f environment.yaml

snakemake –use-conda -c1

#Needs bam-files

[Mon Apr 27 17:31:55 2026] rule delly_p: input: data/fasta/chr22.fasta, data/fasta/chr22.fasta.fai, data/bam/3/T3.bam, data/bam/3/T3.bam.bai, data/bam/3/N3.bam, data/bam/3/N3.bam.bai output: data/bam/3/T3–N3/delly_out/delly-DEL.bcf jobid: 9 wildcards: path=data/bam/3, tumor=T3, normal=N3, sv_type=DEL resources: tmpdir=/tmp, mem_mb=8192, tmp_mb=0

Pipeline Purpose nf-core/mag Metagenome assembly, binning, annotation nf-co.re nf-core/viralrecon Viral genome reconstruction from metagenomic data nf-core/amr Antimicrobial resistance gene detection