Merge branch 'master' of github.com:grunwaldlab/nf-core-plantpathsurveil

nf-core · Aug 3, 2023 · 90e689f · 90e689f
2 parents 211bfee + 5c0c309
commit 90e689f
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diff --git a/bin/sendsketch_filter.R b/bin/sendsketch_filter.R
@@ -2,16 +2,19 @@
 
 # Options
 ani_threshold <- 90
+complt_threshold <- 70
 
 # Parse inputs
 args = commandArgs(trailingOnly = TRUE)
 data <- read.csv(args[1], skip = 2, header = TRUE, sep = '\t')
 
 # Format table
 data$ANI <- as.numeric(sub(pattern = "%", replacement = "", fixed = TRUE, data$ANI))
+data$Complt <- as.numeric(sub(pattern = "%", replacement = "", fixed = TRUE, data$Complt))
 
 # Filter table by match quality
 data <- data[data$ANI > ani_threshold, ]
+data <- data[data$Complt > complt_threshold, ]
 
 # Extract taxon info
 data$genus <- gsub(".*g:(.+);s:.*", "\\1", data$taxonomy)

diff --git a/modules/nf-core/read2tree/main.nf b/modules/nf-core/read2tree/main.nf
diff --git a/modules/nf-core/read2tree/meta.yml b/modules/nf-core/read2tree/meta.yml