From 2bb31740bcdc6a5a2ea1e11e252c4704e197ae36 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 26 Mar 2021 14:08:34 -0600
Subject: [PATCH] Add ONT consolidation script

---
 ont/ont-demux | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 ont/ont-demux

diff --git a/ont/ont-demux b/ont/ont-demux
new file mode 100644
index 0000000..f551131
--- /dev/null
+++ b/ont/ont-demux
@@ -0,0 +1,24 @@
+#!/bin/bash
+# Combines the output from the ONT GridION into a single compressed fastq file
+
+# Initiation, get some important info
+RUNNAME=$(basename "${1}")
+NUMCPU=$(grep -c processor < /proc/cpuinfo)
+OUTNAME="$RUNNAME"_demux
+
+#echo "$RUNNAME"
+#echo "$NUMCPU"
+#echo "$OUTNAME"
+
+# Let guppy do its thing
+guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%
+
+# Unzip the fastqs
+parallel --gnu -j12 --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz
+
+# Squish them together
+cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq
+
+# Rezip the fastqs
+parallel --gnu -j"$NUMCPU" --eta gzip ::: "$OUTNAME"/*/*.fastq
+gzip "$OUTNAME"/"$RUNNAME".fastq