Update count.snake

protect against relative paths to `ln -s` using `readlink`
rnabioco · Oct 15, 2024 · 1b089c1 · 1b089c1
1 parent cc30357
commit 1b089c1
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/rules/count.snake b/rules/count.snake
@@ -148,7 +148,7 @@ rule filter_R1:
   shell:
     """
     if [[ {params.length} == 'False' ]]; then
-      ln -s {input} {output}
+      ln -s $(readlink -f {input}) $(readlink -f {output})
     else
       samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
       samtools index {params.temp}
@@ -212,7 +212,7 @@ rule filter_paired:
   shell:
     """
     if [[ {params.length} == 'False' ]]; then
-      ln -s {input} {output}
+      ln -s $(readlink -f {input}) $(readlink -f {output})
     else
       samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
       samtools index {params.temp}