From d517a934f570427e46be8d83aa2ae4b045b069e8 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 30 Apr 2019 13:05:17 +1000
Subject: Add examples and example README

---
 examples/README.md                         | 30 ++++++++++++++++++++++++++++++
 examples/call.nix                          |  2 +-
 examples/default.nix                       |  2 +-
 examples/ex-nextflow/nextflow-example1.nix |  2 +-
 examples/ex-tnpair/tnpair                  |  2 +-
 examples/ex-tnpair/tnpair.nix              |  4 ++--
 examples/ex-wdl/wdl-scatter-gather.nix     |  2 +-
 7 files changed, 37 insertions(+), 7 deletions(-)
 create mode 100644 examples/README.md

diff --git a/examples/README.md b/examples/README.md
new file mode 100644
index 0000000..66ed04f
--- /dev/null
+++ b/examples/README.md
@@ -0,0 +1,30 @@
+# 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.
+
+## NextFlow and WDL translations
+
+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
+```
+nix build -f nextflow-example1.nix --arg input /path/to/sample.fa
+```
+
+The WDL example requires no extra data and can be built with
+```
+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.
diff --git a/examples/call.nix b/examples/call.nix
index 2b63ae2..212f430 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -2,7 +2,7 @@
 # with the Platypus variant caller. Each input is preprocessed by aligning
 # against a reference genome (defaults to GRCH38), fixing mate information, and
 # marking duplicates. Finally platypus is called over all samples.
-{bionix ? import <bionix> {}
+{bionix ? import ./.. {}
 ,inputs
 ,ref ? null}:
 
diff --git a/examples/default.nix b/examples/default.nix
index d196528..5b3b523 100644
--- a/examples/default.nix
+++ b/examples/default.nix
@@ -1,6 +1,6 @@
 # This example uses the pipelines specified in the call.nix file on the
 # synthetic data in this directory.
-with import <bionix> {};
+with import ./.. {};
 
 let
 
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
index b31984a..0ec1cae 100644
--- a/examples/ex-nextflow/nextflow-example1.nix
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -1,6 +1,6 @@
 # This is a translation of the Nextflow example found at
 # https://www.nextflow.io/example1.html
-{ bionix ? import <bionix> {}
+{ bionix ? import ./../.. {}
 , input ? ./sample.fa}:
 
 with bionix;
diff --git a/examples/ex-tnpair/tnpair b/examples/ex-tnpair/tnpair
index 5b84d5c..d90374b 100755
--- a/examples/ex-tnpair/tnpair
+++ b/examples/ex-tnpair/tnpair
@@ -55,4 +55,4 @@ import ./tnpair.nix {
 }
 EOF
 
-nix build --keep-going "(import ./tnpair-$$)"
+nix build --keep-going "(import ./tnpair-$$)" --no-sandbox
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 2939db4..c42fe95 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -1,5 +1,5 @@
 # This is an example tumour-normal calling pipeline using strelka
-{ bionix ? import <bionix> {}
+{ bionix ? import ./../.. {}
 , normal
 , tumour
 , ref
@@ -20,7 +20,7 @@ let
   ];
 
 in linkDrv [
-  (ln (strelka.call {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
+  (ln (strelka.callSomatic {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
   (ln (preprocess normal) "normal.bam")
   (ln (preprocess tumour) "tumour.bam")
 ]
diff --git a/examples/ex-wdl/wdl-scatter-gather.nix b/examples/ex-wdl/wdl-scatter-gather.nix
index 387d382..61dc441 100644
--- a/examples/ex-wdl/wdl-scatter-gather.nix
+++ b/examples/ex-wdl/wdl-scatter-gather.nix
@@ -1,6 +1,6 @@
 # The scatter-gather example from https://github.com/openwdl/wdl
 # translated to bionix
-{ bionix ? import <bionix> {} }:
+{ bionix ? import ./../.. {} }:
 
 with bionix;
 with lib;
-- 
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