README

# simple.lhs

simple.lhs presents an example workflow using BioShake to align and call
variants. The fastq files are simulated from the reference with some synthetic
variants and included in this directory.

Git-lfs is required to fetch the sequences from the repository (other
tools are also required to run, see [requirements](#requirements)).
After git-lfs is installed, the sequences can be fetched with

  git lfs fetch

The sample pipeline can then be run by:

  runhaskell simple.lhs *.fq

or by compiling then executing the resulting binary on the fastq files. If you
are using stack you can:

  stack setup
  stack build
  stack runhaskell simple.lhs *.fq

There are 3 variants that should be called at positions 14881
(sample2), 29881 (sample1 and sample2) and 44881 (sample 1).

## Requirements

- [git-lfs](https://git-lfs.github.com/)
- [BWA](https://bio-bwa.sourceforge.net/)
- [Samtools](https://github.com/samtools/samtools)
- [platypus](https://github.com/andyrimmer/Platypus)

# nextflow-blast.lhs

This workflow translates a [nextflow
example](https://github.com/nextflow-io/blast-example) to BioShake. The example
shards a FastA file into a number of chunks which are aligned against a
reference database using Blast. The top results are then collected into a final
file. This workflow is an example of a scatter–gather type of workflow. Data is
not provided in this repository.

## Requirements

- [blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)