Merge branch 'develop' into motif2factorsdocs

CHANGELOG.md

@@ -15,6 +15,10 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
   - all samples with a label in the condition column are used
   - (this feature was previously dependent on a batch effect correction in the contrast design)
 
+### Fixed
+
+- (major) regression where peak calling input controls were being ignored.
+
 ## [1.1.0] - 2023-09-13
 
 ### Added

seq2science/rules/peak_calling.smk

@@ -84,7 +84,7 @@ rule genrich_pileup:
         "../envs/genrich.yaml"
     params:
         params=config["peak_caller"].get("genrich", " "),
-        control=lambda wildcards, input: f"-c {input.control}" if "control" in input else "",
+        control=lambda wildcards, input: f"-c {input.control}" if hasattr(input, "control") else "",
         reps=lambda wildcards, input: input,  # help resolve changes in input files
     resources:
         mem_gb=8,
@@ -183,7 +183,7 @@ rule macs2_callpeak:
             )
             else "BAM"
         ),
-        control=lambda wildcards, input: f"-c {input.control}" if "control" in input else "",
+        control=lambda wildcards, input: f"-c {input.control}" if hasattr(input, "control") else "",
         keep_mates=config["macs2_keep_mates"]
     resources:
         mem_gb=4,