From a719ec06337643949bb0a9cbbecb7425340c49af Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 2 Nov 2020 11:11:42 +1100
Subject: star: init

---
 tools/star-align.nix | 38 ++++++++++++++++++++++++++++++++++++++
 tools/star-index.nix | 33 +++++++++++++++++++++++++++++++++
 tools/star.nix       |  8 ++++++++
 3 files changed, 79 insertions(+)
 create mode 100644 tools/star-align.nix
 create mode 100644 tools/star-index.nix
 create mode 100644 tools/star.nix

(limited to 'tools')

diff --git a/tools/star-align.nix b/tools/star-align.nix
new file mode 100644
index 0000000..0cf9ab9
--- /dev/null
+++ b/tools/star-align.nix
@@ -0,0 +1,38 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "star-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "star-input" { fq = _: f; gz = matchFiletype' "star-input" { fq = _: "<(gunzip < ${f})"; }; } f;
+
+in stage {
+  name = "star-align";
+  buildInputs = with pkgs; [ star bc 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
+    STAR ${optionalString (flags != null) flags} \
+     --runThreadN $cores \
+     --genomeDir ${star.index indexAttrs ref} \
+     --readFilesIn ${fq input1} ${optionalString (input2 != null) (fq input2)}
+     ${if bamOutput then "samtools view -b Aligned.out.sam > $out" else "cp Aligned.out.sam $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/star-index.nix b/tools/star-index.nix
new file mode 100644
index 0000000..4bc8399
--- /dev/null
+++ b/tools/star-index.nix
@@ -0,0 +1,33 @@
+{ bionix
+, gtf
+, flags ? null
+, extractSpliceSitesAttrs ? {}
+, extractExonsAttrs ? {}
+, overhang ? 100
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "star-index" { fa = _: true; } ref);
+
+stage {
+  name = "star-index";
+  buildInputs = with pkgs; [ star ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    mkdir $out
+    STAR --runMode genomeGenerate \
+      --runThreadN $NIX_BUILD_CORES \
+      --sjdbGTFfile ${gtf} \
+      --genomeDir $out \
+      --genomeFastaFiles ${ref} \
+      --sjdbOverhang ${toString overhang} \
+      ${optionalString (flags != null) flags}
+  '';
+  passthru.multicore = true;
+  stripStorePaths = false;
+}
diff --git a/tools/star.nix b/tools/star.nix
new file mode 100644
index 0000000..a0a2d58
--- /dev/null
+++ b/tools/star.nix
@@ -0,0 +1,8 @@
+{ bionix }:
+
+with bionix;
+
+{
+  align = callBionixE ./star-align.nix;
+  index = callBionixE ./star-index.nix;
+}
-- 
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