From 8f4b321c07f13ebe8597d1ab4ef3c6bda16f38af Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 9 May 2019 13:42:29 +1000
Subject: fastp: rename run to check for consistency with fastqc

---
 tools/fastp-check.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/fastp-run.nix   | 40 ----------------------------------------
 tools/fastp.nix       |  2 +-
 3 files changed, 41 insertions(+), 41 deletions(-)
 create mode 100644 tools/fastp-check.nix
 delete mode 100644 tools/fastp-run.nix

(limited to 'tools')

diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
new file mode 100644
index 0000000..c7cbb3c
--- /dev/null
+++ b/tools/fastp-check.nix
@@ -0,0 +1,40 @@
+{ bionix
+, flags ? null
+} :
+
+{ input1
+, input2 ? null
+} :
+
+with bionix;
+with pkgs.lib;
+
+# 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 \
+
+                cp fastq2.fq.gz $fastq2
+                ln -s $fastq2 $out/fastq2.fq.gz
+            ''}
+
+            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
diff --git a/tools/fastp-run.nix b/tools/fastp-run.nix
deleted file mode 100644
index c7cbb3c..0000000
--- a/tools/fastp-run.nix
+++ /dev/null
@@ -1,40 +0,0 @@
-{ bionix
-, flags ? null
-} :
-
-{ input1
-, input2 ? null
-} :
-
-with bionix;
-with pkgs.lib;
-
-# 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 \
-
-                cp fastq2.fq.gz $fastq2
-                ln -s $fastq2 $out/fastq2.fq.gz
-            ''}
-
-            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
diff --git a/tools/fastp.nix b/tools/fastp.nix
index 52c9041..90f6c1d 100644
--- a/tools/fastp.nix
+++ b/tools/fastp.nix
@@ -4,6 +4,6 @@ with bionix;
 
 rec {
     app = pkgs.callPackage ./fastp-app.nix {};
-    run = callBionixE ./fastp-run.nix;
+    check = callBionixE ./fastp-check.nix;
 }
 
-- 
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