refactor: move correlation rules to VCF snakefile

Author: ahmig

workflow/rules/report.smk

@@ -282,24 +282,6 @@ rule dnds_plots:
         "../scripts/report/dnds_plots.R"
 
 
-rule af_time_correlation_data:
-    conda: "../envs/renv.yaml"
-    params:
-        cor_method = config["COR"]["METHOD"],
-        cor_exact = config["COR"]["EXACT"],
-    input:
-        variants = OUTDIR/f"{OUTPUT_NAME}.variants.all_sites.tsv",
-        metadata = config["METADATA"],
-    output:
-        fmt_variants = temp(REPORT_DIR_TABLES/"variants.filled.dated.tsv"),
-        correlations = report(REPORT_DIR_TABLES/"af_time_correlation.csv"),
-        subset = REPORT_DIR_TABLES/"af_time_correlation.subset.txt",
-    log:
-        LOGDIR / "af_time_correlation_data" / "log.txt"
-    script:
-        "../scripts/report/af_time_correlation_data.R"
-
-
 rule af_time_correlation_plot:
     conda: "../envs/renv.yaml"
     params:
@@ -335,23 +317,6 @@ rule af_trajectory_panel_plot:
         "../scripts/report/af_trajectory_panel_plot.R"
 
 
-rule pairwise_trajectory_correlation_data:
-    conda: "../envs/renv.yaml"
-    params:
-        cor_method = config["COR"]["METHOD"],
-        cor_use = "pairwise.complete.obs",
-    input:
-        variants = OUTDIR/f"{OUTPUT_NAME}.variants.all_sites.tsv",
-        metadata = config["METADATA"],
-    output:
-        table = REPORT_DIR_TABLES/"pairwise_trajectory_frequency_data.csv",
-        matrix = report(REPORT_DIR_TABLES/"pairwise_trajectory_correlation_matrix.csv"),
-    log:
-        LOGDIR / "pairwise_trajectory_correlation_data" / "log.txt"
-    script:
-        "../scripts/report/pairwise_trajectory_correlation_data.R"
-
-
 rule summary_table:
     conda: "../envs/renv.yaml"
     input:

workflow/rules/vaf.smk

@@ -330,3 +330,38 @@ rule window_zoom_on_feature_data:
         LOGDIR / "window_zoom_on_feature_data" / "{region_name}.log.txt"
     script:
         "../scripts/report/window_zoom_on_feature_data.py"
+
+
+rule af_time_correlation_data:
+    conda: "../envs/renv.yaml"
+    params:
+        cor_method = config["COR"]["METHOD"],
+        cor_exact = config["COR"]["EXACT"],
+    input:
+        variants = OUTDIR/f"{OUTPUT_NAME}.variants.all_sites.tsv",
+        metadata = config["METADATA"],
+    output:
+        fmt_variants = temp(REPORT_DIR_TABLES/"variants.filled.dated.tsv"),
+        correlations = report(REPORT_DIR_TABLES/"af_time_correlation.csv"),
+        subset = REPORT_DIR_TABLES/"af_time_correlation.subset.txt",
+    log:
+        LOGDIR / "af_time_correlation_data" / "log.txt"
+    script:
+        "../scripts/report/af_time_correlation_data.R"
+
+
+rule pairwise_trajectory_correlation_data:
+    conda: "../envs/renv.yaml"
+    params:
+        cor_method = config["COR"]["METHOD"],
+        cor_use = "pairwise.complete.obs",
+    input:
+        variants = OUTDIR/f"{OUTPUT_NAME}.variants.all_sites.tsv",
+        metadata = config["METADATA"],
+    output:
+        table = REPORT_DIR_TABLES/"pairwise_trajectory_frequency_data.csv",
+        matrix = report(REPORT_DIR_TABLES/"pairwise_trajectory_correlation_matrix.csv"),
+    log:
+        LOGDIR / "pairwise_trajectory_correlation_data" / "log.txt"
+    script:
+        "../scripts/report/pairwise_trajectory_correlation_data.R"