move and rename rule

Author: ahmig

workflow/rules/evolution.smk

@@ -14,19 +14,6 @@ rule filter_genbank_features:
         "../scripts/filter_genbank_features.py"
 
 
-rule build_problematic_bed:
-    conda:
-        "../envs/bedtools.yaml"
-    input:
-        vcf = lambda wildcards: select_problematic_vcf(),
-    output:
-        bed = temp(OUTDIR / "sites_masked.bed"),
-    log:
-        LOGDIR / "build_problematic_bed" / "log.txt",
-    shell:
-        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
-
-
 rule n_s_sites:
     threads: 1
     conda: "../envs/biopython.yaml"

workflow/rules/sites.smk

@@ -1,3 +1,16 @@
+rule problematic_vcf_to_bed:
+    conda:
+        "../envs/bedtools.yaml"
+    input:
+        vcf = lambda wildcards: select_problematic_vcf(),
+    output:
+        bed = temp(OUTDIR / "sites_masked.bed"),
+    log:
+        LOGDIR / "build_problematic_bed" / "log.txt",
+    shell:
+        "bedtools merge -i {input.vcf} >{output.bed} 2>{log}"
+
+
 rule bcftools_mpileup_all_sites:
     threads: 1
     conda: "../envs/var_calling.yaml"