linkOutputs: refactor output linking expression

The existing linkDrv only has a singular output, making it difficult to
separate the various types of output. The new functionality replaces the
old with attribute sets defining the outputs.

The old linkDrv is deprecated.

3 files changed, 48 insertions, 49 deletions

diff --git a/default.nix b/default.nix
index 3077470..36dbe44 100644
--- a/default.nix
+++ b/default.nix
@@ -51,19 +51,19 @@ 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;
+    linkOutputs = x: with lib; nixpkgs.stdenvNoCC.mkDerivation {
+      name = "link-outputs";
+      outputs = [ "out" ] ++ attrNames x;
+      nativeBuildInputs = [ pkgs.perl ];
+      buildCommand = let
+        recurse = x: if x ? type && x.type == "derivation" then x else
+          if builtins.typeOf x == "set" then linkOutputs x
+          else error "linkOutputs: unsupported type";
+        link = dst: src: ''
+          ln -s ${recurse src} $(perl -e 'print $ENV{"${dst}"}') ; ln -s ${recurse src} $out/${dst}
+        '';
+      in "mkdir $out \n" + (concatStringsSep "\n" (mapAttrsToList link x));
     };
-    ln = x: y: { src = x; dst = y; };
 
     # Fetching files of specific type
     fetchFastQ = attrs: with types; tagFiletype (filetype.fq {}) (fetchurl attrs);
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index c42fe95..ada96c8 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -19,8 +19,8 @@ let
     (samtools.markdup {})
   ];
 
-in linkDrv [
-  (ln (strelka.callSomatic {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
-  (ln (preprocess normal) "normal.bam")
-  (ln (preprocess tumour) "tumour.bam")
-]
+in linkOutputs {
+  strelka = strelka.callSomatic {} {normal = preprocess normal; tumour = preprocess tumour;};
+  "normal.bam" = preprocess normal;
+  "tumour.bam" = preprocess tumour;
+}
diff --git a/test-tnpair.nix b/test-tnpair.nix
index f90e3a9..afbdf68 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,37 +54,36 @@ let
     plot = cnvkit.scatterPlot {} cnvs;
   };
 
-  testNaming = linkDrv [
-    (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
-    (ln cnvkitResults.cnvs "cnvkit")
-    (ln cnvkitResults.plot "cnvkit.pdf")
-    (ln tnpairResult.octopusVars "octopus.vcf")
-    (ln tnpairResult.octopusSomatic "octopus-somatic.vcf")
-    (ln tnpairResult.variants "strelka")
-    (ln tnpairResult.glvariants "strelka-gl")
-    (ln tnpairResult.variants.indels "strelka.indels.vcf")
-    (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")
-    (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
-    (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3")
-    (ln (samtools.merge {} tnpairResult.shards) "alignments/merged-shards.bam")
-    (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam")
-    (ln (samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)]) "alignments/merged-namesorted.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-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
-    #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
-    #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
-    #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
-    (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}")
-  ];
+  alignments = {
+    "bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files;
+    "bwa-mem.bam" = bwa.mem {inherit ref;} tnpair.normal.files;
+    "bwa-mem2.bam" = bwa.mem2 {inherit ref;} tnpair.normal.files;
+    "minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files;
+    "snap-normal.bam" = snap.align {inherit ref; } tnpair.normal.files;
+    "${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour;
+  };
+
+  testNaming = linkOutputs {
+    facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];};
+    cnvkit = cnvkitResults.cnvs;
+    "cnvkit.pdf" = cnvkitResults.plot;
+    "octopus.vcf" = tnpairResult.octopusVars;
+    "octopus-somatic.vcf" = tnpairResult.octopusSomatic;
+    strelka = tnpairResult.variants;
+    strelka-gl = tnpairResult.glvariants;
+    strelka-indels = tnpairResult.variants.indels;
+    "strelka.snvs.vcf" = tnpairResult.variants.snvs;
+    "strelka.gl.vcf" = tnpairResult.glvariants.variants;
+    gridss = gridss.callVariants {} (with tnpairResult.alignments; [normal tumour]);
+    gridss2 = gridss.call (with tnpairResult.alignments; [normal tumour]);
+    gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour]);
+    "merged-shards.bam" = samtools.merge {} tnpairResult.shards;
+    "merged.bam" = samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal];
+    "merged-namesorted.bam" = samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)];
+    "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour);
+    "${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1;
+    "${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files;
+    inherit alignments;
+  };
 
 in testNaming