Snakemake-Workflows

COLLECTED BY

Organization: Archive Team

Formed in 2009, the Archive Team (not to be confused with the archive.org Archive-It Team) is a rogue archivist collective dedicated to saving copies of rapidly dying or deleted websites for the sake of history and digital heritage. The group is 100% composed of volunteers and interested parties, and has expanded into a large amount of related projects for saving online and digital history.

History is littered with hundreds of conflicts over the future of a community, group, location or business that were "resolved" when one of the parties stepped ahead and destroyed what was there. With the original point of contention destroyed, the debates would fall to the wayside. Archive Team believes that by duplicated condemned data, the conversation and debate can continue, as well as the richness and insight gained by keeping the materials. Our projects have ranged in size from a single volunteer downloading the data to a small-but-critical site, to over 100 volunteers stepping forward to acquire terabytes of user-created data to save for future generations.

The main site for Archive Team is at archiveteam.org and contains up to the date information on various projects, manifestos, plans and walkthroughs.

This collection contains the output of many Archive Team projects, both ongoing and completed. Thanks to the generous providing of disk space by the Internet Archive, multi-terabyte datasets can be made available, as well as in use by the Wayback Machine, providing a path back to lost websites and work.

Our collection has grown to the point of having sub-collections for the type of data we acquire. If you are seeking to browse the contents of these collections, the Wayback Machine is the best first stop. Otherwise, you are free to dig into the stacks to see what you may find.

The Archive Team Panic Downloads are full pulldowns of currently extant websites, meant to serve as emergency backups for needed sites that are in danger of closing, or which will be missed dearly if suddenly lost due to hard drive crashes or server failures.

Collection: Archive Team: URLs

TIMESTAMPS

The Wayback Machine - https://web.archive.org/web/20220130192158/https://github.com/snakemake-workflows

dna-seq-varlociraptor Public
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

Python 49 MIT 23 2 10 Updated Jan 26, 2022
dna-seq-neoantigen-prediction Public
Snakemake workflow for neoantigen prediction

Python 7 MIT 3 8 1 Updated Jan 21, 2022
benchmark-giab Public
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB)

Jupyter Notebook 1 MIT 0 0 0 Updated Jan 17, 2022
rna-seq-kallisto-sleuth Public
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

R 46 MIT 49 6 1 Updated Dec 2, 2021
snakemake-workflow-template Public template
A cookiecutter template for a snakemake-workflow readme file

Python 6 MIT 3 0 0 Updated Dec 1, 2021
rna-seq-star-deseq2 Public
RNA-seq workflow using STAR and DESeq2

Python 201 MIT 161 13 5 Updated Nov 30, 2021
species-quantification Public

Python 2 MIT 0 0 0 Updated Sep 6, 2021
chipseq Public
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

Python 16 MIT 10 0 1 Updated Jul 4, 2021
cite-seq-alevin-fry-seurat Public
Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat

R 2 0 0 0 Updated May 27, 2021
dna-seq-gatk-variant-calling Public
This Snakemake pipeline implements the GATK best-practices workflow

Python 160 MIT 112 10 2 Updated May 5, 2021

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