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Diffstat (limited to 'examples')
| -rw-r--r-- | examples/README.md | 25 |
1 files changed, 13 insertions, 12 deletions
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). + |