# HG changeset patch
# User trungnguyencoffee97ktest
# Date 1654066930 0
# Node ID cc560d7f391a4b73df60ce7c46f679ca797e4d1b

Uploaded a bash file to test

diff -r 000000000000 -r cc560d7f391a nanoclust.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanoclust.sh	Wed Jun 01 07:02:10 2022 +0000
@@ -0,0 +1,24 @@
+#! /bin/bash
+## This code is invented to test NanoporeSanger pipeline, in which we use barrnap to extract 16S ribosomal of bacteria, and use it for taxonomy 
+set -ux
+export THREADS=20
+export nextflow='/media/kt/data/0.Tools/nextflow/nextflow'
+export nanoclust_main='/media/kt/data/TRUNG/2.Tool/NanoCLUST/main.nf'
+export seqtk='/media/kt/data/anaconda3/envs/kt/bin/seqtk'
+export outdir='/media/kt/data/TRUNG/0.Projects/13.NANOPORE-SANGER/3.Output/NanoClust/16SNCBI_REFFSEQ'
+export db16Sncbi='/media/kt/data/TRUNG/2.Tool/NanoCLUST/db/16S_ribosomal_RNA'
+export db16Ssilva_nr_ref='/media/kt/data/TRUNG/3.Database/database_sliva/Nonredundant_Ref/SILVA_138-1_nr_ref'
+export taxdbncbi="/media/kt/data/TRUNG/2.Tool/NanoCLUST/db/taxdb/"
+
+
+longread='/media/kt/data/TRUNG/0.Projects/13.NANOPORE-SANGER/3.Output/Nanopore_reads_of_GCF_000196035.1_ASM19603v1_genomic.trimmed.fastq.gz'
+allreads=''
+for nread in {100,500,1000,1500,2000}; do
+	prefix=$(basename -s .fastq.gz $longread)
+	#capacity=$(awk "BEGIN {print int($nread*1500/10**6+0.5)}")
+	mkdir -p $outdir/${prefix}
+	outread=$outdir/${prefix}/${prefix}_${nread}_reads.fastq.gz
+	$seqtk sample -s50 $longread $nread | gzip > $outread
+    $nextflow $nanoclust_main -profile docker --reads $outread --outdir $outdir/$prefix/${prefix}_${nread}_reads \
+    --db $db16Sncbi --tax $taxdbncbi
+done
\ No newline at end of file