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Allow empty SnpEff flags field #26

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Merged
ahmig merged 1 commit into from
Nov 24, 2025
Merged

Allow empty SnpEff flags field #26

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10 changes: 8 additions & 2 deletions workflow/scripts/format_vcf_fields_longer.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,19 @@ filter.exclude <- lapply(snakemake@params$filter_exclude, empty.to.na)

# Process input table
log_info("Applying filters and writing results")
read_tsv(snakemake@input$tsv) %>%
read_tsv(
snakemake@input$tsv,
col_types = cols(
POS = col_integer(),
.default = col_character()
)
) %>%

# Separate <sep>-delimited "...[*]..." columns (e.g. ANN[*].EFFECT)
separate_rows(
contains("[*]"),
sep = snakemake@params$sep,
convert = TRUE
convert = FALSE
) %>%

# Rename "...[*]..." columns using the provided lookup via Snakemake config
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