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

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Co-authored-by: David Laehnemann <[email protected]>

Author: bilalshaikh42

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