From 0808fc803e3226d2f478229832bb827d7dfcbd0d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Dec 2018 09:55:29 +1100
Subject: link: introduce high-level linking functions

---
 default.nix     | 14 ++++++++++++++
 test-tnpair.nix | 36 +++++++++++++++---------------------
 2 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/default.nix b/default.nix
index 84bb3c8..1e647dd 100644
--- a/default.nix
+++ b/default.nix
@@ -37,6 +37,20 @@ let
     def = f: defs: attrs: f (defs // attrs);
     pipe = let g = fs: with builtins; let h = head fs; t = tail fs; in if t != [] then x: (g t (h x)) else h; in g;
 
+    link = {src, dst}: ''
+      d=$(dirname ${dst})
+      if [ ! -e $out/$d ] ; then
+        mkdir -p $out/$d
+      fi
+      ln -s ${src} $out/${dst}
+    '';
+    mkLinks = nixpkgs.lib.concatMapStringsSep "\n" link;
+    linkDrv = x: nixpkgs.stdenvNoCC.mkDerivation {
+      name = "link";
+      buildCommand = mkLinks x;
+    };
+    ln = x: y: { src = x; dst = y; };
+
     # Fetching files of specific type
     fetchFastQ = attrs: with types; tagFiletype (filetype.fq {}) (fetchurl attrs);
     fetchFastA = attrs: with types; tagFiletype (filetype.fa {}) (fetchurl attrs);
diff --git a/test-tnpair.nix b/test-tnpair.nix
index b01d61e..b897366 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -49,26 +49,20 @@ let
 
   tnpairResult = processPair tnpair;
 
-  testNaming = stdenv.mkDerivation {
-    name = "test-naming";
-    buildCommand = ''
-      mkdir $out
-      ln -s ${tnpairResult.variants} $out/strelka
-      mkdir $out/alignments
-      ln -s ${bowtie.align {inherit ref;} tnpair.normal.files} $out/alignments/bowtie-normal.bam
-      ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])} $out/gridss
-      ln -s ${gridss.call (with tnpairResult.alignments; [normal tumour])} $out/gridss2
-      ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam
-      ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram
-      ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram
-      ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
-      ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat
-      mkdir $out/fastqc
-      ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1
-      ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2
-      ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1
-      ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2
-    '';
-  };
+  testNaming = linkDrv [
+    (ln tnpairResult.variants "strelka")
+    (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
+    (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
+    (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
+    (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam")
+    (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram")
+    (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram")
+    (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat")
+    (ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat")
+    (ln (check tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
+    (ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
+    (ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
+    (ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
+  ];
 
 in testNaming
-- 
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