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-rw-r--r--examples/ex-nextflow/nextflow-example1.nix30
-rwxr-xr-xexamples/ex-tnpair/tnpair (renamed from examples/tnpair)0
-rw-r--r--examples/ex-tnpair/tnpair.nix (renamed from examples/tnpair.nix)0
-rw-r--r--examples/ex-wdl/wdl-scatter-gather.nix33
4 files changed, 63 insertions, 0 deletions
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
new file mode 100644
index 0000000..b31984a
--- /dev/null
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -0,0 +1,30 @@
+# This is a translation of the Nextflow example found at
+# https://www.nextflow.io/example1.html
+{ bionix ? import <bionix> {}
+, input ? ./sample.fa}:
+
+with bionix;
+with lib;
+
+let
+ splitSequences = fa: stage {
+ name = "splitSequences";
+ buildInputs = [ pkgs.gawk ];
+ buildCommand = ''
+ awk '/^>/{f="seq_"++d} {print > f}' ${fa}
+ mkdir $out
+ cp seq* $out
+ '';
+ };
+
+ reverse = fa: stage {
+ name = "reverse";
+ buildCommand = ''
+ ${pkgs.utillinux}/bin/rev ${fa} > $out
+ '';
+ };
+
+in pipe [
+ splitSequences
+ (each reverse)
+] input
diff --git a/examples/tnpair b/examples/ex-tnpair/tnpair
index 5b84d5c..5b84d5c 100755
--- a/examples/tnpair
+++ b/examples/ex-tnpair/tnpair
diff --git a/examples/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 2939db4..2939db4 100644
--- a/examples/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
diff --git a/examples/ex-wdl/wdl-scatter-gather.nix b/examples/ex-wdl/wdl-scatter-gather.nix
new file mode 100644
index 0000000..387d382
--- /dev/null
+++ b/examples/ex-wdl/wdl-scatter-gather.nix
@@ -0,0 +1,33 @@
+# The scatter-gather example from https://github.com/openwdl/wdl
+# translated to bionix
+{ bionix ? import <bionix> {} }:
+
+with bionix;
+with lib;
+
+let
+
+ prepare = splitString "\n" (removeSuffix "\n" (readFile (stage {
+ name = "prepare";
+ buildInputs = [ pkgs.python3 ];
+ buildCommand = ''
+ python -c "print('one\ntwo\nthree\nfour', end=''')" > $out
+ '';
+ })));
+
+ analysis = str: removeSuffix "\n" (readFile (stage {
+ name = "analysis";
+ buildInputs = [ pkgs.python ];
+ buildCommand = ''
+ python -c "print('_${str}_')" > $out
+ '';
+ }));
+
+ gather = strs: stage {
+ name = "gather";
+ buildCommand = ''
+ echo ${concatStringsSep " " strs} > $out
+ '';
+ };
+
+in gather (map analysis prepare)