From 95c8a36a7e673fac090175729069a668daa919da Mon Sep 17 00:00:00 2001
From: l-d-s <l@sdf.org>
Date: Wed, 1 May 2019 14:04:54 +1000
Subject: Add fastp.

---
 tools/fastp-app.nix | 23 +++++++++++++++++++++++
 tools/fastp-run.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/fastp.nix     |  9 +++++++++
 3 files changed, 72 insertions(+)
 create mode 100644 tools/fastp-app.nix
 create mode 100644 tools/fastp-run.nix
 create mode 100644 tools/fastp.nix

(limited to 'tools')

diff --git a/tools/fastp-app.nix b/tools/fastp-app.nix
new file mode 100644
index 0000000..bb716e2
--- /dev/null
+++ b/tools/fastp-app.nix
@@ -0,0 +1,23 @@
+{ stdenv
+, fetchFromGitHub
+, zlib 
+}:
+
+stdenv.mkDerivation rec {
+  name = "fastp-${version}";
+  version = "0.20.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenGene";
+    repo = "fastp";
+    rev = "v${version}";
+    sha256 = "0y0qfp3j3gqnmlqskna8x43acss21vxwck287c4fagxlcaba0s30";
+  };
+
+  buildInputs = [ zlib ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp fastp $out/bin
+  '';
+}
diff --git a/tools/fastp-run.nix b/tools/fastp-run.nix
new file mode 100644
index 0000000..c7cbb3c
--- /dev/null
+++ b/tools/fastp-run.nix
@@ -0,0 +1,40 @@
+{ bionix
+, flags ? null
+} :
+
+{ input1
+, input2 ? null
+} :
+
+with bionix;
+with pkgs.lib;
+
+# Match input file type—how to do .fq and .fq.gz? Does bz2 work?
+
+stage {
+    name = "fastp";
+    buildInputs = [ fastp.app ];
+    outputs = [ "out" "fastq1" "fastq2" "html" "json" ];
+    buildCommand = ''
+        mkdir -p $out
+        fastp \
+            ${optionalString (flags != null) flags} \
+            -i ${input1} \
+            -o fastq1.fq.gz \
+            ${optionalString (input2 != null) ''
+                -I ${input2} \
+                -O fastq2.fq.gz \
+
+                cp fastq2.fq.gz $fastq2
+                ln -s $fastq2 $out/fastq2.fq.gz
+            ''}
+
+            cp fastq1.fq.gz $fastq1
+            cp fastp.html $html
+            cp fastp.json $json
+
+            ln -s $fastq1 $out/fastq1.fq.gz
+            ln -s $html $out/fastp.html
+            ln -s $json $out/fastp.json
+    '';
+}
\ No newline at end of file
diff --git a/tools/fastp.nix b/tools/fastp.nix
new file mode 100644
index 0000000..52c9041
--- /dev/null
+++ b/tools/fastp.nix
@@ -0,0 +1,9 @@
+{ bionix }:
+
+with bionix;
+
+rec {
+    app = pkgs.callPackage ./fastp-app.nix {};
+    run = callBionixE ./fastp-run.nix;
+}
+
-- 
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