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-rw-r--r--tools/minimap2-align.nix37
-rw-r--r--tools/minimap2.nix10
2 files changed, 47 insertions, 0 deletions
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix
new file mode 100644
index 0000000..14c88a5
--- /dev/null
+++ b/tools/minimap2-align.nix
@@ -0,0 +1,37 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, preset
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+ fa = f: matchFiletype "minmap2-ref" { fa = _: f; } f;
+ fq = f: matchFiletype "minmap2-input" { fq = _: f; gz = matchFiletype' "minmap2-input" { fq = _: f; }; } f;
+
+in stage {
+ name = "minmap2-align";
+ buildInputs = with pkgs; [ minimap2 bc ] ++ optional bamOutput samtools;
+ buildCommand = ''
+ ln -s ${fa ref} ref.fa
+ cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+ if [[ $cores -lt 1 ]] ; then
+ cores=1
+ fi
+ minimap2 ${optionalString (flags != null) flags} -t $cores -ax ${preset} 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/minimap2.nix b/tools/minimap2.nix
new file mode 100644
index 0000000..e1d6af5
--- /dev/null
+++ b/tools/minimap2.nix
@@ -0,0 +1,10 @@
+{ bionix }:
+
+with bionix;
+
+rec {
+ /* Align read against a reference
+ * Type: align :: {ref :: fasta, bamOutput :: bool, preset :: string, ...} -> {input1, input2} -> bam/sam
+ */
+ align = callBionixE ./minimap2-align.nix;
+}