Fix samples configuation

CHANGELOG.md

@@ -1,5 +1,10 @@
 All notable changes to MoGAAAP will be documented in this file.
 
+## [Unreleased]
+
+### Changed
+- Allow for not listing the optional columns in the sample sheet (#131).
+
 ## [1.2.1 - 2026-03-11]
 
 ### Changed

MoGAAAP/workflow/rules/3.quality_assessment/00.proteome.smk

@@ -4,7 +4,7 @@ rule get_proteome:
         annotation = "final_output/{asmname}.full.gff",
         config = "results/{asmname}/agat_config.yaml",
     output:
-        "results/{asmname}/3.quality_assessment/proteome.pep.fa",
+        ensure("results/{asmname}/3.quality_assessment/proteome.pep.fa"), non_empty=True),
     log:
         "results/logs/3.quality_assessment/proteome/{asmname}.log",
     benchmark:

MoGAAAP/workflow/rules/common.smk

@@ -52,19 +52,25 @@ def get_best_wgstype(asmname):
     return "HiFi"
 
 def has_hifi(asmname): #false is only possible when an assembly is provided
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["hifi"].isnull().values.item()
+    if "hifi" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["hifi"].isnull().values.item()
+    return False
 
 def get_hifi(wildcards):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(wildcards.asmname)]["hifi"].values.item().split(";")
 
 def has_ont(asmname):
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["ont"].isnull().values.item()
+    if "ont" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["ont"].isnull().values.item()
+    return False
 
 def get_ont(wildcards):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(wildcards.asmname)]["ont"].values.item().split(";")
 
 def has_illumina(asmname):
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["illumina_1"].isnull().values.item()
+    if "illumina_1" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["illumina_1"].isnull().values.item()
+    return False
 
 def get_illumina_1(wildcards):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(wildcards.asmname)]["illumina_1"].values.item()
@@ -73,7 +79,9 @@ def get_illumina_2(wildcards):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(wildcards.asmname)]["illumina_2"].values.item()
 
 def has_hic(asmname):
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["hic_1"].isnull().values.item()
+    if "hic_1" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["hic_1"].isnull().values.item()
+    return False
 
 def get_hic_1(wildcards):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(wildcards.asmname)]["hic_1"].values.item()
@@ -97,13 +105,17 @@ def get_reference_id(asmname):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["referenceId"].values.item()
 
 def has_assembly_location(asmname):
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["assemblyLocation"].isnull().values.item()
+    if "assemblyLocation" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["assemblyLocation"].isnull().values.item()
+    return False
 
 def get_assembly_location(asmname):
     return SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["assemblyLocation"].values.item()
 
 def has_annotation_location(asmname):
-    return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["annotationLocation"].isnull().values.item()
+    if "annotationLocation" in SAMPLES:
+        return not SAMPLES[SAMPLES["accessionId"] == get_clean_accession_id(asmname)]["annotationLocation"].isnull().values.item()
+    return False
 
 def get_annotation_location(asmname):
     """