From 61e3984e8126f19302f1a4804733066cf194f903 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Wed, 17 Jan 2024 13:09:47 +0100
Subject: [PATCH] Update samplesheet.csv

---
 assets/samplesheet.csv | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 5f653ab..1dd25b8 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,5 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,run_accession,instrument_platform,fastq_1,fastq_2,kraken2_report,kraken2_classifiedout,centrifuge_out,centrifuge_result,diamond
+SRR13439790,SRR13439790,ILLUMINA,assets/data/SRR13439790_SRR13439790.unmapped_1.fastq.gz,assets/data/SRR13439790_SRR13439790.unmapped_2.fastq.gz,assets/data/SRR13439790_pe_SRR13439790_k2_pluspf.kraken2.kraken2.report.txt,assets/data/SRR13439790_pe_SRR13439790_k2_pluspf.kraken2.kraken2.classifiedreads.txt,assets/data/SRR13439790_pe_SRR13439790_p_compressed+h+v.centrifuge.txt,assets/data/SRR13439790_pe_SRR13439790_p_compressed+h+v.centrifuge.results.txt,assets/data/SRR13439790_pe_SRR13439790_diamond.diamond.tsv
+SRR13439802,SRR13439802,ILLUMINA,assets/data/SRR13439802_SRR13439802.unmapped_1.fastq.gz,assets/data/SRR13439802_SRR13439802.unmapped_2.fastq.gz,assets/data/SRR13439802_pe_SRR13439802_k2_pluspf.kraken2.kraken2.report.txt,assets/data/SRR13439802_pe_SRR13439802_k2_pluspf.kraken2.kraken2.classifiedreads.txt,assets/data/SRR13439802_pe_SRR13439802_p_compressed+h+v.centrifuge.txt,assets/data/SRR13439802_pe_SRR13439802_p_compressed+h+v.centrifuge.results.txt,assets/data/SRR13439802_pe_SRR13439802_diamond.diamond.tsv
+SRR13439813,SRR13439813,ILLUMINA,assets/data/SRR13439813_SRR13439813.unmapped_1.fastq.gz,assets/data/SRR13439813_SRR13439813.unmapped_2.fastq.gz,assets/data/SRR13439813_pe_SRR13439813_k2_pluspf.kraken2.kraken2.report.txt,assets/data/SRR13439813_pe_SRR13439813_k2_pluspf.kraken2.kraken2.classifiedreads.txt,assets/data/SRR13439813_pe_SRR13439813_p_compressed+h+v.centrifuge.txt,assets/data/SRR13439813_pe_SRR13439813_p_compressed+h+v.centrifuge.results.txt,assets/data/SRR13439813_pe_SRR13439813_diamond.diamond.tsv
+SRR13439799,SRR13439799,OXFORD_NANOPORE,assets/data/SRR13439799_SRR13439799.unmapped_other.fastq.gz,,assets/data/SRR13439799_se_SRR13439799_k2_pluspf.kraken2.kraken2.report.txt,assets/data/SRR13439799_se_SRR13439799_k2_pluspf.kraken2.kraken2.classifiedreads.txt,assets/data/SRR13439799_se_SRR13439799_p_compressed+h+v.centrifuge.txt,assets/data/SRR13439799_se_SRR13439799_p_compressed+h+v.centrifuge.results.txt,assets/data/SRR13439799_se_SRR13439799_diamond.diamond.tsv