From 0809ce0f2c95262a866e218eb5033c558700c0ec Mon Sep 17 00:00:00 2001
From: BethYates <113996036+BethYates@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:40:54 +0100
Subject: [PATCH 1/2] Update input_check.nf

pass quoteoption to splitCSV operator to allow handling of samplesheets from fetchngs which use double quotes around values.
---
 subworkflows/local/input_check.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index da522ca8..d498269f 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -20,7 +20,7 @@ workflow INPUT_CHECK {
     if ( params.fetchngs_samplesheet ) {
         FETCHNGSSAMPLESHEET_CHECK ( samplesheet )
             .csv
-            .splitCsv ( header:true, sep:',' )
+            .splitCsv ( header:true, sep:',', quote:'"' )
             .branch { row ->
                 paired: row.fastq_2
                     [[id: row.run_accession, row:row], [row.fastq_1, row.fastq_2]]

From a8e2bbaedc410f5a64df4a0c7c174151823945ac Mon Sep 17 00:00:00 2001
From: BethYates <113996036+BethYates@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:53:38 +0100
Subject: [PATCH 2/2] Update CHANGELOG.md

Added fix to fetchngs samplesheet parsing in INPUT_CHECK.nf
---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d2a81c5..7792d887 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ General tidy up of the configuration and the pipeline
 - Removed some options that were not used or not needed
 - All relevant outputs are now copied to the output directory
 - Fixed some blast parameters to match the behaviour of the Snakemake pipeline
+- Fixed parsing of samplesheets from fetchngs to capture correct data type
 
 ### Parameters