Revert "fix: seperate paired and single ended rules, conditionally im…

…port" This reverts commit e61eac0.
OpenOmics · Dec 10, 2024 · d51d903 · d51d903
1 parent e61eac0
commit d51d903
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Showing 12 changed files with 691 additions and 1,023 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -221,18 +221,9 @@ rule all:
     input:
         rule_all_ins
 
-# Include endedness rules
-if paired_end:
-    include: join("rules", "paired", "peakcall.smk")
-    include: join("rules", "paired", "qc.smk")
-    include: join("rules", "paired", "trim.smk")
-else:
-    include: join("rules", "paired", "peakcall.smk")
-    include: join("rules", "paired", "qc.smk")
-    include: join("rules", "paired", "trim.smk")
-
-# Include general rules
+# Include child rules
 include: join("rules", "hooks.smk")
+include: join("rules", "trim_align_dedup.smk")
 include: join("rules", "qc.smk")
 include: join("rules", "peakcall.smk")
 include: join("rules", "dba.smk")

diff --git a/workflow/rules/paired/peakcall.smk b/workflow/rules/paired/peakcall.smk
diff --git a/workflow/rules/paired/qc.smk b/workflow/rules/paired/qc.smk