compression: refactor compression framework

5 files changed, 63 insertions, 25 deletions

diff --git a/tools/compression-bunzip2.nix b/tools/compression-bunzip2.nix
new file mode 100644
index 0000000..06fe682
--- /dev/null
+++ b/tools/compression-bunzip2.nix
@@ -0,0 +1,12 @@
+{bionix}:
+
+with bionix;
+
+input:
+
+stage {
+  name = "bunzip2";
+  buildInputs = with pkgs; [ bzip2 ];
+  buildCommand = "bunzip2 < ${input} > $out";
+  passthru.filetype = types.bunzip2 input;
+}
diff --git a/tools/compression-bzip2.nix b/tools/compression-bzip2.nix
new file mode 100644
index 0000000..6dfb749
--- /dev/null
+++ b/tools/compression-bzip2.nix
@@ -0,0 +1,12 @@
+{bionix}:
+
+with bionix;
+
+input:
+
+stage {
+  name = "bzip2";
+  buildInputs = with pkgs; [ bzip2 ];
+  buildCommand = "bzip2 < ${input} > $out";
+  passthru.filetype = filetype.bz2 input.filetype;
+}
diff --git a/tools/compression-gunzip.nix b/tools/compression-gunzip.nix
new file mode 100644
index 0000000..6c98f91
--- /dev/null
+++ b/tools/compression-gunzip.nix
@@ -0,0 +1,12 @@
+{bionix}:
+
+with bionix;
+
+input:
+
+stage {
+  name = "gunzip";
+  buildInputs = with pkgs; [ gzip ];
+  buildCommand = "gunzip < ${input} > $out";
+  passthru.filetype = types.gunzip input;
+}
diff --git a/tools/compression-gzip.nix b/tools/compression-gzip.nix
new file mode 100644
index 0000000..50fca9e
--- /dev/null
+++ b/tools/compression-gzip.nix
@@ -0,0 +1,12 @@
+{bionix}:
+
+with bionix;
+
+input:
+
+stage {
+  name = "gzip";
+  buildInputs = with pkgs; [ gzip ];
+  buildCommand = "gzip < ${input} > $out";
+  passthru.filetype = filetype.gzip input.filetype;
+}
diff --git a/tools/compression.nix b/tools/compression.nix
index 6e69d7e..bfcc292 100644
--- a/tools/compression.nix
+++ b/tools/compression.nix
@@ -1,9 +1,15 @@
 {bionix}:
 
 with bionix;
+with types;
 
-{
-  uncompress = f: types.matchFiletype "uncompress" {
+let
+  gzip = callBionixE ./compression-gzip.nix;
+  gunzip = callBionixE ./compression-gunzip.nix;
+  bunzip2 = callBionixE ./compression-bunzip2.nix;
+
+in {
+  uncompress = attrs: f: matchFiletype "uncompress" {
     fa = _: f;
     fq = _: f;
     bam = _: f;
@@ -11,23 +17,12 @@ with bionix;
     cram = _: f;
     vcf = _: f;
     bed = _: f;
-    gz = _: types.tagFiletype (types.gunzip f.filetype) (stage {
-      name = "gunzip";
-      buildCommand = "gunzip < ${f} > $out";
-    });
-    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stage {
-      name = "bunzip2";
-      buildCommand = "bunzip2 < ${f} > $out";
-    });
-  } f.filetype;
+    gz = _: gunzip attrs f;
+    bz2 = _: bunzip2 attrs f;
+  } f;
 
-  gzip = f:
-    let
-      gz = (stage {
-        name = "gzip";
-        buildCommand = "gzip < ${f} > $out";
-        passthru = { filetype = types.filetype.gz f.filetype; };
-      });
+  gzip = attrs: f:
+    let gz = gzip attrs f;
     in types.matchFiletype "compressed" {
       fa = _: gz;
       fq = _: gz;
@@ -39,13 +34,8 @@ with bionix;
       gz = x: x;
     } f;
 
-  bzip2 = f:
-    let
-      bz2 = (stage {
-        name = "bzip2";
-        buildCommand = "bzip2 < ${f} > $out";
-        passthru = { filetype = types.filetype.bz2 f.filetype; };
-      });
+  bzip2 = attrs: f:
+    let bz2 = bzip2 attrs f;
     in types.matchFiletype "compressed" {
       fa = _: gz;
       fq = _: gz;