fix: correct query function to provide both the ip and control if req…

…uested

seqnado/design.py

@@ -480,26 +480,39 @@ def controls_performed(self) -> List[str]:
                 control.add(f.control_performed)
         return list(control)
 
-    def query(self, sample_name: str) -> FastqSetIP:
+    def query(self, sample_name: str, full_experiment: bool = False) -> Union[FastqSetIP, Dict[str, FastqSetIP]]:
         """
         Extracts a pair of fastq files from the design.
         """
         ip_names = set(f.ip_set_fullname for f in self.experiments)
         control_names = set(
             f.control_fullname for f in self.experiments if f.has_control
         )
+        is_control = False
+
+        experiment_files = dict()
 
         if sample_name in ip_names or sample_name in control_names:
             for experiment in self.experiments:
                 if experiment.ip_set_fullname == sample_name:
-                    return experiment.ip
+                    experiment_files["ip"] = experiment.ip
+                    experiment_files["control"] = experiment.control
+
                 elif (
                     experiment.has_control
                     and experiment.control_fullname == sample_name
                 ):
-                    return experiment.control
+                    is_control = True
+                    experiment_files["ip"] = experiment.ip
+                    experiment_files["control"] = experiment.control
         else:
             raise ValueError(f"Could not find sample with name {sample_name}")
+
+
+        if full_experiment:
+            return experiment_files
+        else:
+            return experiment_files["ip"] if not is_control else experiment_files["control"]
 
     @classmethod
     def from_fastq_files(cls, fq: List[Union[str, pathlib.Path]], **kwargs):

seqnado/workflow/rules/peak_call_chip.smk

@@ -25,37 +25,27 @@ def format_macs_options(wildcards, options):
         return options
 
 
-def get_control_bam(wildcards):
-    exp = DESIGN.query(sample_name=f"{wildcards.sample}_{wildcards.treatment}")
-    if exp:
-        control = f"seqnado_output/aligned/{wildcards.sample}_{exp.ip_or_control_name}.bam"
-    else:
-        control = "UNDEFINED"
-    return control
-
-
-def get_control_tag(wildcards):
-    exp = DESIGN.query(sample_name=f"{wildcards.sample}_{wildcards.treatment}")
-    if not exp:
-        control = "UNDEFINED"
-    else:
-        control = f"seqnado_output/tag_dirs/{wildcards.sample}_{exp.ip_or_control_name}"
-    return control
-
-
-def get_control_bigwig(wildcards):
-    exp = DESIGN.query(sample_name=f"{wildcards.sample}_{wildcards.treatment}")
-    if not exp:
-        control = "UNDEFINED"
-    else:
-        control = f"seqnado_output/bigwigs/deeptools/unscaled/{wildcards.sample}_{exp.ip_or_control_name}.bigWig"
-    return control
+def get_control_file(wildcards, file_type: Literal["bam", "tag", "bigwig"], allow_null=False):
+    exp = DESIGN.query(sample_name=f"{wildcards.sample}_{wildcards.treatment}", full_experiment=True)
+
+    if not exp["control"] and not allow_null: # if control is not defined, return UNDEFINED. This is to prevent the rule from running
+        return "UNDEFINED"
+    elif not exp["control"] and allow_null: # if control is not defined, return empty list
+        return []
+
+    match file_type:
+        case "bam":
+            return f"seqnado_output/aligned/{exp['control'].name}.bam"
+        case "tag":
+            return f"seqnado_output/tag_dirs/{exp['control'].name}"
+        case "bigwig":
+            return f"seqnado_output/bigwigs/deeptools/unscaled/{exp['control'].name}.bigWig"
 
 
 rule macs2_with_input:
     input:
         treatment="seqnado_output/aligned/{sample}_{treatment}.bam",
-        control=get_control_bam,
+        control=lambda wc: get_control_file(wc, file_type="bam", allow_null=False),
     output:
         peaks="seqnado_output/peaks/macs/{sample}_{treatment}.bed",
     params:
@@ -78,7 +68,7 @@ rule macs2_with_input:
 rule macs2_no_input:
     input:
         treatment="seqnado_output/aligned/{sample}_{treatment}.bam",
-        control=lambda wc: [] if get_control_bam(wc) == "UNDEFINED" else get_control_bam(wc), 
+        control=lambda wc: get_control_file(wc, file_type="bam", allow_null=True), 
     output:
         peaks="seqnado_output/peaks/macs/{sample}_{treatment}.bed",
     params:
@@ -101,7 +91,7 @@ rule macs2_no_input:
 rule homer_with_input:
     input:
         treatment="seqnado_output/tag_dirs/{sample}_{treatment}",
-        control=get_control_tag,
+        control=lambda wc: get_control_file(wc, file_type="tag", allow_null=False),
     output:
         peaks="seqnado_output/peaks/homer/{sample}_{treatment}.bed",
     log:
@@ -123,7 +113,7 @@ rule homer_with_input:
 rule homer_no_input:
     input:
         treatment="seqnado_output/tag_dirs/{sample}_{treatment}",
-        control=lambda wc: [] if get_control_tag(wc) == "UNDEFINED" else get_control_tag(wc),
+        control=lambda wc: get_control_file(wc, file_type="tag", allow_null=True),
     output:
         peaks="seqnado_output/peaks/homer/{sample}_{treatment}.bed",
     log:
@@ -145,7 +135,7 @@ rule homer_no_input:
 rule lanceotron_with_input:
     input:
         treatment="seqnado_output/bigwigs/deeptools/unscaled/{sample}_{treatment}.bigWig",
-        control=get_control_bigwig,
+        control=lambda wc: get_control_file(wc, file_type="bigwig", allow_null=False),
     output:
         peaks="seqnado_output/peaks/lanceotron/{sample}_{treatment}.bed",
     log:
@@ -170,7 +160,7 @@ rule lanceotron_with_input:
 rule lanceotron_no_input:
     input:
         treatment="seqnado_output/bigwigs/deeptools/unscaled/{sample}_{treatment}.bigWig",
-        control=lambda wc: [] if get_control_bigwig(wc) == "UNDEFINED" else get_control_bigwig(wc),
+        control=lambda wc: get_control_file(wc, file_type="bigwig", allow_null=False),
     output:
         peaks="seqnado_output/peaks/lanceotron/{sample}_{treatment}.bed",
     log: