From 6c470d3a54fb922f37e4129da7b70864186cee03 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 14 Dec 2021 14:08:49 +1100
Subject: subread: init

---
 default.nix             |  1 +
 test-tnpair.nix         |  1 +
 tools/subread-align.nix | 38 ++++++++++++++++++++++++++++++++++++++
 tools/subread-index.nix | 20 ++++++++++++++++++++
 tools/subread.nix       |  8 ++++++++
 5 files changed, 68 insertions(+)
 create mode 100644 tools/subread-align.nix
 create mode 100644 tools/subread-index.nix
 create mode 100644 tools/subread.nix

diff --git a/default.nix b/default.nix
index 6f6fb3d..8d262f7 100644
--- a/default.nix
+++ b/default.nix
@@ -51,6 +51,7 @@ let
       whisper = callBionix ./tools/whisper.nix { };
       star = callBionix ./tools/star.nix { };
       genmap = callBionix ./tools/genmap.nix { };
+      subread = callBionix ./tools/subread.nix { };
 
       slurm-run = callPackage ./lib/slurm.nix { };
       slurm-exec = f: x: y:
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 0960b6f..8da1207 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -57,6 +57,7 @@ let
 
   alignments = {
     "bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
+    "subread.bam" = subread.align { inherit ref; } tnpair.normal.files;
     "last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
     "whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
     "bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
diff --git a/tools/subread-align.nix b/tools/subread-align.nix
new file mode 100644
index 0000000..0b0f4c1
--- /dev/null
+++ b/tools/subread-align.nix
@@ -0,0 +1,38 @@
+{ bionix
+, ref
+, flags ? null
+, indexAttrs ? { }
+, RG ? { }
+, type ? 1
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "subread-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "subread-input" { fq = _: f; gz = matchFiletype' "subread-input" { fq = _: f; }; } f;
+
+in
+stage {
+  name = "subread-align";
+  buildInputs = with pkgs; [ subread ];
+  buildCommand = ''
+    subread-align -i ${bionix.subread.index indexAttrs ref}/ref ${optionalString (flags != null) flags} -T $NIX_BUILD_CORES \
+      -t ${toString type} \
+      -r ${fq input1} \
+      ${optionalString (input2 != null) "-R ${fq input2}"} \
+      ${optionalString (RG ? ID) ''
+        --rg-id ${RG.ID} ${concatMapAttrsStringsSep " " (k: v: "--rg ${k}:${v}") (filterAttrs (k: _: k != "ID") RG)} \
+      ''} \
+      -o $out
+  '';
+  passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
+  passthru.multicore = true;
+}
diff --git a/tools/subread-index.nix b/tools/subread-index.nix
new file mode 100644
index 0000000..a5177a1
--- /dev/null
+++ b/tools/subread-index.nix
@@ -0,0 +1,20 @@
+{ bionix
+, flags ? null
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "subread-index" { fa = _: true; } ref);
+
+stage {
+  name = "subread-index";
+  buildInputs = with pkgs; [ subread ];
+  buildCommand = ''
+    mkdir $out
+    subread-buildindex ${optionalString (flags != null) flags} -o $out/ref ${ref}
+  '';
+}
diff --git a/tools/subread.nix b/tools/subread.nix
new file mode 100644
index 0000000..3ac563a
--- /dev/null
+++ b/tools/subread.nix
@@ -0,0 +1,8 @@
+{ bionix }:
+
+with bionix;
+
+{
+  align = callBionixE ./subread-align.nix;
+  index = callBionixE ./subread-index.nix;
+}
-- 
cgit v1.2.3