From b0eb2beb334015b471ab7a1e7a42de70f3e5f839 Mon Sep 17 00:00:00 2001
From: tannevaled <david.delavennat@polytechnique.edu>
Date: Sun, 21 Jun 2026 07:00:19 +0200
Subject: [PATCH 1/2] new(github.com/OpenGene/fastp): fastp

Ultra-fast FASTQ preprocessor (C++). isa-l+libdeflate+highway+zlib; gcc14 build + libstdcxx runtime; inline fixture.
---
 .../github.com/OpenGene/fastp/package.yml     | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 projects/github.com/OpenGene/fastp/package.yml

diff --git a/projects/github.com/OpenGene/fastp/package.yml b/projects/github.com/OpenGene/fastp/package.yml
new file mode 100644
index 0000000000..a4dc7b9a64
--- /dev/null
+++ b/projects/github.com/OpenGene/fastp/package.yml
@@ -0,0 +1,47 @@
+distributable:
+  url: https://github.com/OpenGene/fastp/archive/refs/tags/{{version.tag}}.tar.gz
+  strip-components: 1
+
+versions:
+  github: OpenGene/fastp
+
+dependencies:
+  github.com/intel/isa-l: ^2
+  github.com/ebiggers/libdeflate: ^1
+  google.com/highway: ^1
+  zlib.net: ^1
+  linux:
+    gnu.org/gcc/libstdcxx: 14
+
+build:
+  dependencies:
+    freedesktop.org/pkg-config: "*"
+    linux:
+      gnu.org/gcc: 14
+  script:
+    - mkdir -p "{{prefix}}/bin"
+    - make CXX=c++ $ARGS
+    - make install $ARGS
+  env:
+    ARGS:
+      - PREFIX="{{prefix}}"
+
+provides:
+  - bin/fastp
+
+test:
+  - run: (fastp --version 2>&1 || true) | grep "{{version}}"
+  - run: |
+      fastp -i $FIXTURE -o out.fq --disable_adapter_trimming
+      test -s out.fq
+    fixture:
+      extname: fq
+      content: |
+        @r1
+        ACGTACGTACGTACGTACGTACGTACGTACGT
+        +
+        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+        @r2
+        TTTTGGGGCCCCAAAATTTTGGGGCCCCAAAA
+        +
+        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

From 1099d0677f22c28dc176b4267e2596448e6d4d9e Mon Sep 17 00:00:00 2001
From: Jacob Heider <jacob@pkgx.dev>
Date: Sun, 21 Jun 2026 16:42:30 -0400
Subject: [PATCH 2/2] Refactor package.yml by updating dependencies and tests

Remove unnecessary dependency and streamline test commands.
---
 projects/github.com/OpenGene/fastp/package.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/projects/github.com/OpenGene/fastp/package.yml b/projects/github.com/OpenGene/fastp/package.yml
index a4dc7b9a64..1c4af3e792 100644
--- a/projects/github.com/OpenGene/fastp/package.yml
+++ b/projects/github.com/OpenGene/fastp/package.yml
@@ -15,7 +15,6 @@ dependencies:
 
 build:
   dependencies:
-    freedesktop.org/pkg-config: "*"
     linux:
       gnu.org/gcc: 14
   script:
@@ -30,10 +29,8 @@ provides:
   - bin/fastp
 
 test:
-  - run: (fastp --version 2>&1 || true) | grep "{{version}}"
-  - run: |
-      fastp -i $FIXTURE -o out.fq --disable_adapter_trimming
-      test -s out.fq
+  - (fastp --version 2>&1 || true) | grep "{{version}}"
+  - run: fastp -i $FIXTURE -o out.fq --disable_adapter_trimming
     fixture:
       extname: fq
       content: |
@@ -45,3 +42,4 @@ test:
         TTTTGGGGCCCCAAAATTTTGGGGCCCCAAAA
         +
         IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+  - test -s out.fq