bwa-mem2: init

5 files changed, 86 insertions, 2 deletions

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 0e13338..76fcfab 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -62,6 +62,8 @@ let
     (ln tnpairResult.variants.snvs "strelka.snvs.vcf")
     (ln tnpairResult.glvariants.variants "strelka.gl.vcf")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
+    (ln (bwa.mem {inherit ref;} tnpair.normal.files) "alignments/bwa-mem.bam")
+    (ln (bwa.mem2 {inherit ref;} tnpair.normal.files) "alignments/bwa-mem2.bam")
     (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam")
     (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
diff --git a/tools/bwa-index2.nix b/tools/bwa-index2.nix
new file mode 100644
index 0000000..f5cc69b
--- /dev/null
+++ b/tools/bwa-index2.nix
@@ -0,0 +1,23 @@
+{ bionix
+, flags ? null
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "bwa-index" { fa = _: true; } ref);
+
+stage {
+  name = "bwa-index2";
+  buildInputs = with pkgs; [ bionix.bwa.app2 ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    bwa-mem2 index ${optionalString (flags != null) flags} ref.fa
+    mkdir $out
+    mv ref.fa.* $out
+    grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true
+  '';
+}
diff --git a/tools/bwa-mem2-app.nix b/tools/bwa-mem2-app.nix
new file mode 100644
index 0000000..8cca5a5
--- /dev/null
+++ b/tools/bwa-mem2-app.nix
@@ -0,0 +1,15 @@
+{ bwa, fetchFromGitHub }:
+  bwa.overrideAttrs (_:
+    {
+      name = "bwa-mem2";
+      src = fetchFromGitHub {
+        owner = "bwa-mem2";
+        repo = "bwa-mem2";
+        rev = "f882015f7f46845f72c10094a621264f78d206d8";
+        sha256 = "1wfx8j9mwbb29jw4zxp28lajmj774jy1l5x229nf065cqr2dgyqg";
+        };
+      installPhase = ''
+        mkdir -p $out/bin
+        cp bwa-mem2 $out/bin
+        '';
+      })
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
new file mode 100644
index 0000000..3de1944
--- /dev/null
+++ b/tools/bwa-mem2.nix
@@ -0,0 +1,40 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+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-mem2";
+  buildInputs = with pkgs; [ bionix.bwa.app2 bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    ln -s ${fa ref} ref.fa
+    for f in ${bionix.bwa.index2 indexAttrs ref}/* ; do
+      ln -s $f
+    done
+    cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+    if [[ $cores -lt 1 ]] ; then
+      cores=1
+    fi
+    bwa-mem2 mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
+      ${optionalString bamOutput "| samtools view -b"} \
+      > $out
+  '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.multicore = true;
+}
diff --git a/tools/bwa.nix b/tools/bwa.nix
index 58f9651..90a8bd3 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -3,15 +3,19 @@
 with bionix;
 
 rec {
+  app2 = pkgs.callPackage ./bwa-mem2-app.nix {};
+
   /* Align read against a reference: defaults to bwa-mem */
-  align = bwa-mem;
+  align = bionix.bwa.mem;
 
   /* Align reads against a reference using bwa-mem
   Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
   */
-  bwa-mem = callBionixE ./bwa-mem.nix;
+  mem = callBionixE ./bwa-mem.nix;
+  mem2 = callBionixE ./bwa-mem2.nix;
   /* Creates an reference index for BWA
   Type: index :: {...} -> fasta -> BWA index
   */
   index = callBionixE ./bwa-index.nix;
+  index2 = callBionixE ./bwa-index2.nix;
 }