Refactor module load and add comments to conf

pipelines/annotations.snakefile

@@ -28,13 +28,17 @@ merge_nthreads = int(config.get("merge_nthreads") or 64)
 
 # If modules are used we load them here
 load_bfc = " ".join(
-    [config["bcftools_load_cmd"], "&&" if config["bcftools_load_cmd"] else ""]
+    [config["bcftools_load_cmd"], "&&" if config.get("bcftools_load_cmd") else ""]
 )
 load_hts = " ".join(
-    [config["htslib_load_cmd"], "&&" if config["htslib_load_cmd"] else ""]
+    [config["htslib_load_cmd"], "&&" if config.get("htslib_load_cmd") else ""]
+)
+load_perl = " ".join(
+    [config["perl_load_cmd"], "&&" if config.get("perl_load_cmd") else ""]
+)
+load_vep = " ".join(
+    [config["vep_load_cmd"], "&&" if config.get("vep_load_cmd") else ""]
 )
-load_perl = " ".join([config["perl_load_cmd"], "&&" if config["perl_load_cmd"] else ""])
-load_vep = " ".join([config["vep_load_cmd"], "&&" if config["vep_load_cmd"] else ""])
 
 
 # init data path

pipelines/config/deeprvat_annotation_config.yaml

@@ -1,13 +1,16 @@
 fasta_dir : reference
 fasta_file_name : hg38.fa
-bcftools_load_cmd : module load bcftools/1.9
-htslib_load_cmd : module load htslib/1.9
-perl_load_cmd : module load perl/5.20.2
-vep_load_cmd : module load vep/108.1
+# Uncomment to use module load for required tools
+#bcftools_load_cmd : module load bcftools/1.9
+#htslib_load_cmd : module load htslib/1.9
+#perl_load_cmd : module load perl/5.20.2
+#vep_load_cmd : module load vep/108.1
 
 source_variant_file_pattern : test_vcf_data_c{chr}_b{block}
 source_variant_file_type: 'vcf.gz'
-included_chromosomes : ['21','22']
+
+# Uncomment to select subset of chromosomes
+#included_chromosomes : ['21','22']
 
 metadata_dir : input_dir/vcf/metadata
 pvcf_blocks_file : pvcf_blocks.txt