This is a list of example workflows exemplifying the use of Cuneiform for different use cases. All workflows come in the form of a Chef cookbook, which automatically sets up the workflow, fetches all input data, and sets up all necessary tools.
Machine Learning and Information Retrieval
- Jul 31, 2016 Word Count https://github.com/joergen7/wordcount This workflow counts the occurrences of words in a text corpus. It implements a Cuneiform example workflow first published in Bux et al. 2015.
Bioinformatics and Next-Generation Sequencing
- Jun 30, 2016 Phylogeny https://github.com/joergen7/phylogeny This workflow performs a phylogenetic study of the CHASE domain, a protein domain resposible for cytokinin reception in the two-component system in late diverging plants. It is a reimplementation of a paper by Pils and Heyl 2009.
- May 9, 2016 GC Count https://github.com/joergen7/gccount This workflow calculates the percentage of GC content in a given sequence file in FastA format. It is based on an example workflow in SciPipe by Samuel Lampa.
- Apr 29, 2016 ChIP-Seq https://github.com/joergen7/chip-seq This workflow demonstrates ChIP-Seq analysis in Escherichia coli by performing peak detection in a treatment sample using MACS. It is a Cuneiform transcription of a hands-on introduction to ChIP-Seq by Morgane Thomas-Chollier which itself is based on a study by Myers et al. 2013.
- Mar 31, 2016 Variant Calling (GATK) https://github.com/joergen7/variant-call-gatk This workflow uses GATK to call germline variants in a sequence sample. In two extra VQSR steps for both SNPs and indels common variants are filtered out. This workflow reimplements a study by van der Auwera et al. 2013.
- Feb 26, 2016 RNA-Seq https://github.com/joergen7/rna-seq This workflow exemplifies the comparison of DNA expression levels in two experimental conditions from RNA-Seq data. It reimplements a study by Trapnell et al. 2012.
- Jan 12, 2016 Variant Calling (VarScan) https://github.com/joergen7/variant-call This workflow calls variants in a sequence sample by aligning it to a reference genome, identifying variants and annotating them. It reimplements a publication by Koboldt et al. 2013.
- Dec 30, 2015 Methylation Analysis https://github.com/joergen7/methylation This workflow compares a case and a control sample identifying differences in DNA methylation. It reimplements a publication by Hansen et al. 2012.