From d12f635279ec1b43a57293c9c95919a489606d8c Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 11 Jun 2019 16:44:36 +1000 Subject: rewrite README documentation Significant expansion of README to include installation instructions and instructions on how to use with HPC. --- examples/README.md | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) (limited to 'examples') diff --git a/examples/README.md b/examples/README.md index 66ed04f..1689709 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,17 +1,14 @@ # Bionix examples -This directory has a few example workflows in bionix along with example data. -A basic workflow is defined in `call.nix`, and an example of applying it to the -sample data is in `default.nix`. To build the `default.nix` workflow, run -``` -nix build -``` -from this directory. +This directory has a few example workflows in bionix along with example +data. A basic workflow is defined in `call.nix`, and an example of +applying it to the sample data is in `default.nix`. To build the +`default.nix` workflow, run ```nix build``` from this directory. ## NextFlow and WDL translations -The directories `ex-nextflow` and `ex-wdl` contain translated examples from the -NextFlow and WDL documentation respectively. +The directories `ex-nextflow` and `ex-wdl` contain translated examples +from the NextFlow and WDL documentation respectively. The NextFlow translated example does not come with example data. It can be built with ``` @@ -25,6 +22,10 @@ nix build -f wdl-scatter-gather.nix ## Example script wrapper -`ex-tnpair` contains a shell script based example on how a front-end for users -might be constructed. It is a simple tumour-normal somatic calling workflow -using the Strelka variant caller. +`ex-tnpair` contains a shell script based example on how a front-end for +users might be constructed. It is a simple tumour-normal somatic calling +workflow using the Strelka variant caller. The script accepts a +reference fasta along with paired normal and tumor fastq files and +performs alignment, preprocessing, and variant calling with +[`strelka`](https://github.com/Illumina/strelka). + -- cgit v1.2.3