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.

---
 default.nix         |  1 +
 test-tnpair.nix     | 12 +++++++-----
 tools/fastp-app.nix | 23 +++++++++++++++++++++++
 tools/fastp-run.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/fastp.nix     |  9 +++++++++
 5 files changed, 80 insertions(+), 5 deletions(-)
 create mode 100644 tools/fastp-app.nix
 create mode 100644 tools/fastp-run.nix
 create mode 100644 tools/fastp.nix

diff --git a/default.nix b/default.nix
index 608fa9b..d67f2eb 100644
--- a/default.nix
+++ b/default.nix
@@ -33,6 +33,7 @@ let
     snpeff = callBionix ./tools/snpeff.nix {};
     strelka = callBionix ./tools/strelka.nix {};
     ascat = callBionix ./tools/ascat.nix {};
+    fastp = callBionix ./tools/fastp.nix {};
 
     sbatch = attrs: bionix.extend (self: super: with self; rec {
       sbatchDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; } // attrs;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 1d281fa..1b5f347 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -14,7 +14,8 @@ let
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
-  check = fastqc.check {};
+  check-fastqc = fastqc.check {};
+  check-fastp = fastp.run {};
   callVariants = strelka.callSomatic {};
   markdup = samtools.markdup {};
   fixmate = samtools.fixmate {};
@@ -59,10 +60,11 @@ let
     #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram")
     (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat")
     #(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat")
-    (ln (check tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
-    #(ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
-    #(ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
-    #(ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
+    (ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
+    #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
+    #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
+    #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
+    (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}")
   ];
 
 in testNaming
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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