--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ab1_fastq.R	Wed Jan 12 15:12:58 2022 +0000
@@ -0,0 +1,35 @@
+#Rscript
+
+############################################
+##      Convert ab1 files into fastq      ##
+############################################
+
+#####Packages
+
+library(CrispRVariants, quietly = TRUE)
+library(sangerseqR, quietly = TRUE)
+
+#####Load arguments
+
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) == 0) {
+    stop("This tool needs at least one argument")
+} else {
+    file <- args[1]
+    filename <- args[2]
+    tr <- as.logical(args[3])
+    co <- as.numeric(args[4])
+    min_seq <- as.integer(args[5])
+    os <- as.numeric(args[6])
+}
+
+##### Conversion
+
+if (grepl("^.+\\.[aA][bB][1i]$", filename)) {
+    nfile <- sub("^(.+)\\.[aA][bB][1i]$", "\\1", filename)
+} else {
+    nfile <- filename
+}
+
+CrispRVariants::abifToFastq(nfile, file, "output.fastq", trim = tr, cutoff = co, min_seq_len = min_seq, offset = os)