refactor: work around bug in snakefmt that adds two lines after each …

…include by moving an if statement into common.smk (#578)

* refactor: work around bug in snakefmt that adds two lines after each include by moving an if statement into common.smk

* more refactoring

workflow/Snakefile

@@ -24,12 +24,6 @@ container: "docker://condaforge/mambaforge"
 containerized: "quay.io/uncovar/uncovar#0.15.1"
 
 
-if config["strain-calling"]["use-gisaid"]:
-
-    envvars:
-        "GISAID_API_TOKEN",
-
-
 include: "rules/common.smk"
 include: "rules/benchmarking_common.smk"
 include: "rules/utils.smk"
@@ -47,17 +41,15 @@ include: "rules/variant_filtration.smk"
 include: "rules/variant_report.smk"
 include: "rules/generate_output.smk"
 include: "rules/benchmarking.smk"
+include: "rules/long_read.smk"
+include: "rules/lineage_variant_calling.smk"
 
 
 if config["data-handling"]["use-data-handling"]:
 
     include: "rules/preprocessing.smk"
 
 
-include: "rules/long_read.smk"
-include: "rules/lineage_variant_calling.smk"
-
-
 if config["data-handling"]["archive-data"]:
 
     rule save_latest_run:

workflow/rules/common.smk

@@ -11,8 +11,18 @@ import urllib.request
 from snakemake.utils import validate
 
 
+if config["strain-calling"]["use-gisaid"]:
+
+    envvars:
+        "GISAID_API_TOKEN",
+
+
 VARTYPES = ["SNV", "MNV", "INS", "DEL", "REP", "INV", "DUP"]
+
+
 ILLUMINA_VARRANGE = ["small", "structural"]
+
+
 ONT_VARRANGE = ["homopolymer-medaka", "homopolymer-longshot"]
 ION_VARRANGE = ["small", "structural"]