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authorJustin Bedo <cu@cua0.org>2019-04-30 13:05:17 +1000
committerJustin Bedo <cu@cua0.org>2019-04-30 13:05:17 +1000
commitd517a934f570427e46be8d83aa2ae4b045b069e8 (patch)
treef419839a9405b0e252f0e7753623fe2c52c5d447 /examples
parent5d03ab8afa1803ddabc7616a48fff9889e3a0c51 (diff)
Add examples and example README
Diffstat (limited to 'examples')
-rw-r--r--examples/README.md30
-rw-r--r--examples/call.nix2
-rw-r--r--examples/default.nix2
-rw-r--r--examples/ex-nextflow/nextflow-example1.nix2
-rwxr-xr-xexamples/ex-tnpair/tnpair2
-rw-r--r--examples/ex-tnpair/tnpair.nix4
-rw-r--r--examples/ex-wdl/wdl-scatter-gather.nix2
7 files changed, 37 insertions, 7 deletions
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;