feat: remove demix module from rule core (#30)

* feat: remove demix module from rule core

* fix: add demix include call for tests

* feat: remove pangolin module from rule core

Author: ahmig

.test/Snakefile

@@ -12,7 +12,9 @@ __version__ = "1.3.0"
 
 # Rules
 include: "../workflow/core.smk"
+include: "../workflow/rules/demix.smk"
 include: "../workflow/rules/context.smk"
+include: "../workflow/rules/pangolin.smk"
 include: "../workflow/rules/report.smk"
 
 rule all:

workflow/Snakefile

@@ -16,6 +16,8 @@ configfile: "config/targets.yaml"
 
 include: "core.smk"
 include: "rules/context.smk"
+include: "rules/demix.smk"
+include: "rules/pangolin.smk"
 include: "rules/report.smk"
 
 rule all:

workflow/core.smk

@@ -16,8 +16,6 @@ REPORT_DIR_TABLES = Path(OUTDIR/"report/tables")
 include: "rules/fetch.smk"
 include: "rules/fasta.smk"
 include: "rules/asr.smk"
-include: "rules/demix.smk"
 include: "rules/vaf.smk"
-include: "rules/pangolin.smk"
 include: "rules/distances.smk"
 include: "rules/evolution.smk"