Update selected columns

Author: ahmig

config/config.yaml

@@ -51,16 +51,6 @@ ANNOTATION:
       - WARNING_TRANSCRIPT_NO_START_CODON
       - WARNING_TRANSCRIPT_NO_STOP_CODON
   VARIANT_NAME_PATTERN: "{GENE}:{coalesce(HGVS_P, HGVS_C)}"  # dplyr's coalesce finds the first non-missing element
-  SELECT_COLS:
-    - CHROM
-    - POS
-    - REF
-    - ALT
-    - EFFECT
-    - IMPACT
-    - GENE
-    - HGVS_P
-    - HGVS_C
 DEMIX:
   PATHOGEN: "SARS-CoV-2"
   MIN_QUALITY: 20

workflow/rules/vaf.smk

@@ -198,7 +198,6 @@ rule merge_annotation:
     conda: "../envs/renv.yaml"
     params:
         ref_name = config["ALIGNMENT_REFERENCE"],
-        select_columns = config["ANNOTATION"]["SELECT_COLS"],
     input:
         tsv = OUTDIR/"vaf"/"{sample}.masked.prefiltered.tsv",
         annot = OUTDIR/"vaf"/"{sample}.vcf_fields.longer.tsv",

workflow/scripts/merge_annotation.R

@@ -39,7 +39,12 @@ log_info("Reading annotation table")
 annotation <- read_tsv(
   snakemake@input$annot,
   col_select = c(
-    unlist(snakemake@params$select_columns),
+    "CHROM",
+    "POS",
+    "REF",
+    "ALT",
+    "EFFECT",
+    "IMPACT",
     "VARIANT_NAME"
   ),
   col_types = list(