From 7b7f7c5eddfb3829cef8df7bf217d8309507cf2d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 21 May 2019 18:20:24 +1000
Subject: fastp: split outputs and set filetypes

---
 tools/fastp-check.nix | 50 +++++++++++++++++++++++++-------------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
index c7cbb3c..be807d6 100644
--- a/tools/fastp-check.nix
+++ b/tools/fastp-check.nix
@@ -8,33 +8,33 @@
 
 with bionix;
 with pkgs.lib;
+with types;
 
 # Match input file type—how to do .fq and .fq.gz? Does bz2 work?
 
-stage {
-    name = "fastp";
-    buildInputs = [ fastp.app ];
-    outputs = [ "out" "fastq1" "fastq2" "html" "json" ];
-    buildCommand = ''
-        mkdir -p $out
-        fastp \
-            ${optionalString (flags != null) flags} \
-            -i ${input1} \
-            -o fastq1.fq.gz \
-            ${optionalString (input2 != null) ''
-                -I ${input2} \
-                -O fastq2.fq.gz \
+let
+  out =
+    stage {
+        name = "fastp";
+        buildInputs = [ fastp.app ];
+        outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else []);
+        buildCommand = ''
+            mkdir -p $out
+            fastp \
+                ${optionalString (flags != null) flags} \
+                -i ${input1} \
+                -o fastq1.fq.gz \
+                ${optionalString (input2 != null) ''
+                    -I ${input2} \
+                    -O fastq2.fq.gz \
 
-                cp fastq2.fq.gz $fastq2
-                ln -s $fastq2 $out/fastq2.fq.gz
-            ''}
+                    cp fastq2.fq.gz $fastq2
+                ''}
 
-            cp fastq1.fq.gz $fastq1
-            cp fastp.html $html
-            cp fastp.json $json
-
-            ln -s $fastq1 $out/fastq1.fq.gz
-            ln -s $html $out/fastp.html
-            ln -s $json $out/fastp.json
-    '';
-}
\ No newline at end of file
+                cp fastq1.fq.gz $fastq1
+                cp fastp.html $out
+                cp fastp.json $json
+        '';
+    };
+  fqgz = { filetype = filetype.gz (filetype.fastq {}); };
+in out // { fastq1 = out.fastq1 // fqgz; } // (if input2 != null then {fastq2 = out.fastq2 // fqgz; } else {})
-- 
cgit v1.2.3


From b714521422af63a910ff660dcc019cbaeb6a5d17 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 21 May 2019 18:23:02 +1000
Subject: fastp: input filetypes

---
 tools/fastp-check.nix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
index be807d6..bd522d8 100644
--- a/tools/fastp-check.nix
+++ b/tools/fastp-check.nix
@@ -7,12 +7,12 @@
 } :
 
 with bionix;
-with pkgs.lib;
+with lib;
 with types;
 
-# Match input file type—how to do .fq and .fq.gz? Does bz2 work?
-
 let
+  fq = f: matchFiletype "fastp-input" { fq = _: f; gz = matchFiletype' "fastp-input" { fq = _: f; }; } f;
+
   out =
     stage {
         name = "fastp";
@@ -22,10 +22,10 @@ let
             mkdir -p $out
             fastp \
                 ${optionalString (flags != null) flags} \
-                -i ${input1} \
+                -i ${fq input1} \
                 -o fastq1.fq.gz \
                 ${optionalString (input2 != null) ''
-                    -I ${input2} \
+                    -I ${fq input2} \
                     -O fastq2.fq.gz \
 
                     cp fastq2.fq.gz $fastq2
-- 
cgit v1.2.3


From a7b06b941b30feaf8b3b0e0ad1bc986d58d9f9ac Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 4 Jun 2019 18:53:09 +1000
Subject: strip: handle non-buildCommand based stages

---
 default.nix | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/default.nix b/default.nix
index 15b8d87..450118d 100644
--- a/default.nix
+++ b/default.nix
@@ -77,8 +77,8 @@ let
     lib = nixpkgs.lib // { types = types; shard = callBionix ./lib/shard.nix {};};
     stage = x@{ name, stripStorePaths ? true, multicore ? false, ... }:
       (if stripStorePaths then strip else x: x) (nixpkgs.stdenvNoCC.mkDerivation (x // {name = "bionix-" + name; inherit multicore;}));
-    strip = drv: drv.overrideAttrs (attrs: {
-      buildCommand = attrs.buildCommand + ''
+    strip = drv: let
+        stripCommand = ''
 
         function rewrite {
           sed -i 's|/nix/store/[^-]*|/nix/store/00000000000000000000000000000000|g' $1
@@ -96,7 +96,12 @@ let
           rewriteOutput $o
         done
       '';
-    });
+      in drv.overrideAttrs (attrs:
+        if attrs ? buildCommand then
+          {buildCommand = attrs.buildCommand + stripCommand;}
+        else
+          { fixupPhase = (if attrs ? fixupPhase then attrs.fixupPhase else "") + stripCommand; }
+        );
 
     # splitting/joining
     splitFile = file: drv: stage {
-- 
cgit v1.2.3