fix: use derived input for star_index (#81)

* 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 * chore: make the formatter happy --------- Co-authored-by: David Laehnemann <[email protected]>
snakemake-workflows · Jun 5, 2024 · 87fffe6 · 87fffe6
1 parent b3998c1
commit 87fffe6
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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