From 1416a55e40bdf426f2112878f6bb468af3722cf2 Mon Sep 17 00:00:00 2001
From: Bilal Shaikh <bilalshaikh42@gmail.com>
Date: Tue, 4 Jun 2024 12:52:54 -0400
Subject: [PATCH] fix: use derived input for star_index

the file path for the -sjdbGTFfile parameter was hardcoded to 'resources/genome.gtf' which causes execution to fail due to missing files on remote execution environments without a shared filesystem (such as kubernetes)

This derives the filepath correctly from the input property to fix this issue
---
 workflow/rules/ref.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 9be480ba..8ee0fd6b 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -63,7 +63,7 @@ rule star_index:
         directory("resources/star_genome"),
     threads: 4
     params:
-        extra="--sjdbGTFfile resources/genome.gtf --sjdbOverhang 100",
+        extra= lambda wc, input: f'--sjdbGTFfile {input.annotation} --sjdbOverhang 100',
     log:
         "logs/star_index_genome.log",
     cache: True