Add fastp.

1 files changed, 40 insertions, 0 deletions

diff --git a/tools/fastp-run.nix b/tools/fastp-run.nix
new file mode 100644
index 0000000..c7cbb3c
--- /dev/null
+++ b/tools/fastp-run.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