From a1d18efc18772a233aa759b622c3a9960824f109 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 30 Apr 2019 09:47:49 +1000
Subject: cleanup examples and stray files

---
 examples/ex-nextflow/nextflow-example1.nix | 30 ++++++++++++++++
 examples/ex-tnpair/tnpair                  | 58 ++++++++++++++++++++++++++++++
 examples/ex-tnpair/tnpair.nix              | 26 ++++++++++++++
 examples/ex-wdl/wdl-scatter-gather.nix     | 33 +++++++++++++++++
 examples/tnpair                            | 58 ------------------------------
 examples/tnpair.nix                        | 26 --------------
 6 files changed, 147 insertions(+), 84 deletions(-)
 create mode 100644 examples/ex-nextflow/nextflow-example1.nix
 create mode 100755 examples/ex-tnpair/tnpair
 create mode 100644 examples/ex-tnpair/tnpair.nix
 create mode 100644 examples/ex-wdl/wdl-scatter-gather.nix
 delete mode 100755 examples/tnpair
 delete mode 100644 examples/tnpair.nix

(limited to 'examples')

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/ex-tnpair/tnpair b/examples/ex-tnpair/tnpair
new file mode 100755
index 0000000..5b84d5c
--- /dev/null
+++ b/examples/ex-tnpair/tnpair
@@ -0,0 +1,58 @@
+#!/bin/sh
+
+set -e
+
+if [[ $# -ne 5 ]] ; then
+    echo "Usage: $0 ref normal1 normal2 tumour1 tumour2"
+    exit 1
+fi
+
+function cleanup {
+    if [[ -e tnpair-$$ ]]; then
+        rm tnpair-$$
+    fi
+}
+trap cleanup INT TERM EXIT
+
+ref=`readlink -f $1`
+norm1=`readlink -f $2`
+norm2=`readlink -f $3`
+tumour1=`readlink -f $4`
+tumour2=`readlink -f $5`
+
+refhash=`nix-hash --base32 --type sha256 --flat $ref`
+norm1hash=`nix-hash --base32 --type sha256 --flat $norm1`
+norm2hash=`nix-hash --base32 --type sha256 --flat $norm2`
+tumour1hash=`nix-hash --base32 --type sha256 --flat $tumour1`
+tumour2hash=`nix-hash --base32 --type sha256 --flat $tumour2`
+
+cat > tnpair-$$ <<EOF
+import ./tnpair.nix {
+    normal = {
+        input1={
+            url="file://$norm1";
+            sha256="$norm1hash";
+        };
+        input2={
+            url="file://$norm2";
+            sha256="$norm2hash";
+        };
+    };
+    tumour = {
+        input1={
+            url = "file://$tumour1";
+            sha256 = "$tumour1hash";
+        };
+        input2={
+            url = "file://$tumour2";
+            sha256 = "$tumour2hash";
+        };
+    };
+    ref = {
+        url = "file://$ref";
+        sha256 = "$refhash";
+    };
+}
+EOF
+
+nix build --keep-going "(import ./tnpair-$$)"
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
new file mode 100644
index 0000000..2939db4
--- /dev/null
+++ b/examples/ex-tnpair/tnpair.nix
@@ -0,0 +1,26 @@
+# This is an example tumour-normal calling pipeline using strelka
+{ bionix ? import <bionix> {}
+, normal
+, tumour
+, ref
+}:
+
+with bionix;
+with lib;
+
+let
+  input = mapAttrs (_: fetchFastQGZ);
+
+  preprocess = pipe [
+    input
+    (bwa.align { ref = fetchFastA ref; })
+    (samtools.fixmate {})
+    (samtools.sort {})
+    (samtools.markdup {})
+  ];
+
+in linkDrv [
+  (ln (strelka.call {} {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
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)
diff --git a/examples/tnpair b/examples/tnpair
deleted file mode 100755
index 5b84d5c..0000000
--- a/examples/tnpair
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/sh
-
-set -e
-
-if [[ $# -ne 5 ]] ; then
-    echo "Usage: $0 ref normal1 normal2 tumour1 tumour2"
-    exit 1
-fi
-
-function cleanup {
-    if [[ -e tnpair-$$ ]]; then
-        rm tnpair-$$
-    fi
-}
-trap cleanup INT TERM EXIT
-
-ref=`readlink -f $1`
-norm1=`readlink -f $2`
-norm2=`readlink -f $3`
-tumour1=`readlink -f $4`
-tumour2=`readlink -f $5`
-
-refhash=`nix-hash --base32 --type sha256 --flat $ref`
-norm1hash=`nix-hash --base32 --type sha256 --flat $norm1`
-norm2hash=`nix-hash --base32 --type sha256 --flat $norm2`
-tumour1hash=`nix-hash --base32 --type sha256 --flat $tumour1`
-tumour2hash=`nix-hash --base32 --type sha256 --flat $tumour2`
-
-cat > tnpair-$$ <<EOF
-import ./tnpair.nix {
-    normal = {
-        input1={
-            url="file://$norm1";
-            sha256="$norm1hash";
-        };
-        input2={
-            url="file://$norm2";
-            sha256="$norm2hash";
-        };
-    };
-    tumour = {
-        input1={
-            url = "file://$tumour1";
-            sha256 = "$tumour1hash";
-        };
-        input2={
-            url = "file://$tumour2";
-            sha256 = "$tumour2hash";
-        };
-    };
-    ref = {
-        url = "file://$ref";
-        sha256 = "$refhash";
-    };
-}
-EOF
-
-nix build --keep-going "(import ./tnpair-$$)"
diff --git a/examples/tnpair.nix b/examples/tnpair.nix
deleted file mode 100644
index 2939db4..0000000
--- a/examples/tnpair.nix
+++ /dev/null
@@ -1,26 +0,0 @@
-# This is an example tumour-normal calling pipeline using strelka
-{ bionix ? import <bionix> {}
-, normal
-, tumour
-, ref
-}:
-
-with bionix;
-with lib;
-
-let
-  input = mapAttrs (_: fetchFastQGZ);
-
-  preprocess = pipe [
-    input
-    (bwa.align { ref = fetchFastA ref; })
-    (samtools.fixmate {})
-    (samtools.sort {})
-    (samtools.markdup {})
-  ];
-
-in linkDrv [
-  (ln (strelka.call {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
-  (ln (preprocess normal) "normal.bam")
-  (ln (preprocess tumour) "tumour.bam")
-]
-- 
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