From d75b723281aea944fbafdb28f5b0841a03827b4a Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 6 Dec 2021 17:23:47 +1100
Subject: parameterise RG line as nix attribute set

Allows more seamless transitioning between alingment algorithms
---
 default.nix              | 3 ++-
 tools/bowtie-align.nix   | 5 ++++-
 tools/bwa-mem.nix        | 3 ++-
 tools/bwa-mem2.nix       | 2 ++
 tools/minimap2-align.nix | 2 ++
 5 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/default.nix b/default.nix
index db5d14f..6f6fb3d 100644
--- a/default.nix
+++ b/default.nix
@@ -109,7 +109,7 @@ let
               '';
             in
             ''
-              mkdir $out 
+              mkdir $out
             '' + (concatStringsSep "\n" (mapAttrsToList link x));
           passthru.linkInputs = x;
         };
@@ -136,6 +136,7 @@ let
       lib = nixpkgs.lib // {
         inherit types;
         shard = callBionix ./lib/shard.nix { };
+        concatMapAttrsStringsSep = s: f: a: with nixpkgs.lib; concatStringsSep s (mapAttrsToList f a);
       };
       stage = x@{ name, stripStorePaths ? true, multicore ? false, ... }:
         (if stripStorePaths then strip else x: x)
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 8df3dba..cca12a2 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -3,6 +3,7 @@
 , bamOutput ? true
 , flags ? null
 , indexAttrs ? { }
+, RG ? { }
 }:
 
 { input1
@@ -29,7 +30,9 @@ stage {
     fi
     bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \
       ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \
-      | samtools sort -n \
+      ${optionalString (RG ? ID) ''
+        --rg-id ${RG.ID} ${concatMapAttrsStringsSep " " (k: v: "--rg ${k}:${v}") (filterAttrs (k: _: k != "ID") RG)} \
+      ''} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 52e73d1..84038d9 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -3,6 +3,7 @@
 , bamOutput ? true
 , flags ? null
 , indexAttrs ? { }
+, RG ? { }
 }:
 
 { input1
@@ -17,7 +18,6 @@ with compression;
 let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
-
 in
 stage {
   name = "bwa-mem";
@@ -33,6 +33,7 @@ stage {
     fi
     bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
+      ${optionalString (RG ? ID) "-R'@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
index 843c5b0..e6237f0 100644
--- a/tools/bwa-mem2.nix
+++ b/tools/bwa-mem2.nix
@@ -3,6 +3,7 @@
 , bamOutput ? true
 , flags ? null
 , indexAttrs ? { }
+, RG ? { }
 }:
 
 { input1
@@ -33,6 +34,7 @@ stage {
     fi
     bwa-mem2 mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
+      ${optionalString (RG ? ID) "-R'@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix
index 18bca35..e7e71c6 100644
--- a/tools/minimap2-align.nix
+++ b/tools/minimap2-align.nix
@@ -3,6 +3,7 @@
 , bamOutput ? true
 , flags ? null
 , preset
+, RG ? { }
 }:
 
 { input1
@@ -30,6 +31,7 @@ stage {
     fi
     minimap2 ${optionalString (flags != null) flags} -t $cores -ax ${preset} ref.fa ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
+      ${optionalString (RG ? ID) "-R'@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-- 
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