From 6b8fa28dff1449fa7127d48ffa8b558c287987d9 Mon Sep 17 00:00:00 2001
From: Fattigman <jacob.karlstrom@gmail.com>
Date: Wed, 21 Jun 2023 11:57:21 +0200
Subject: [PATCH 1/2] citeseq compatible with illumina v2

---
 examples/CTG_SampleSheet.csv | 6 +++---
 modules/split_sheet/main.nf  | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/examples/CTG_SampleSheet.csv b/examples/CTG_SampleSheet.csv
index 21db48b..2f21196 100644
--- a/examples/CTG_SampleSheet.csv
+++ b/examples/CTG_SampleSheet.csv
@@ -28,12 +28,12 @@ sample-15,human,project8,n,n,n,atac,scatac-10x,n,n,n,n,n
 sample-16,human,project9,n,n,4,atac,scarc-10x,n,n,n,n,n
 sample-17,human,project9,n,n,4,gex,scarc-10x,n,n,n,n,n
 sample-18,human,project10,n,n,n,gex,scvisium-10x,cytaimage,darkimage,image,slide,slide_area
-[10X_Flex_Settings],,,,,,,,
+[FlexConfig_Data],,,,,,,,
 sample_id,probe_barcode,Sample_Source,,,,,,
 sample1,BC001|BC002,sample_7,,,,,,
 sample1,BC003|BC004,sample-8,,,,,,
-[10X_FeatureReference],,,,,,,,
-id,name,read,pattern,sequence,feature_type,Sample_Source,,
+[FeatureReference_Data],,,,,,,,
+id,name,read,pattern,sequence,feature_type,Sample_ID,,
 ADT_C0014,HuMs.CD11b,R2,5PNNNNNNNNNN(BC),TGAAGGCTCATTTGT,ADT,sample-4|sample-7,,
 ADT_C0073,HuMs.CD44,R2,5PNNNNNNNNNN(BC),TGGCTTCAGGTCCTA,ADT,sample-4|sample-7,,
 ADT_C0103,HuMs.CD45R_B220,R2,5P(BC),CCTACACCTCATAAT,ADT,sample-4|sample-7,,
diff --git a/modules/split_sheet/main.nf b/modules/split_sheet/main.nf
index db3b082..1424139 100644
--- a/modules/split_sheet/main.nf
+++ b/modules/split_sheet/main.nf
@@ -5,8 +5,8 @@ process SPLITSHEET {
     output:
         path "10X_Data.csv", emit: data
         path "Data.csv", emit: pipe_data, optional: true
-        path "10X_Flex_Settings.csv", emit: flex, optional: true
-        path "10X_FeatureReference.csv", emit: feature_reference, optional: true
+        path "FlexConfig_Data.csv", emit: flex, optional: true
+        path "FeatureReference_Data.csv", emit: feature_reference, optional: true
     shell:
     '''
     while read line; do

From 14cc6b201abf945b55470b20faa1650eb56f7690 Mon Sep 17 00:00:00 2001
From: Fattigman <jacob.karlstrom@gmail.com>
Date: Wed, 21 Jun 2023 11:58:08 +0200
Subject: [PATCH 2/2] updated manifest version

---
 templates/manifest.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/manifest.html b/templates/manifest.html
index ad8fcc7..de45f21 100644
--- a/templates/manifest.html
+++ b/templates/manifest.html
@@ -83,7 +83,7 @@
     <div class="main-block">
       <div class="block-item">
         <h1><b>Nextflow manifest</b></h1>
-        <p> <b>Pipeline release:</b> 1.1.0</p>
+        <p> <b>Pipeline release:</b> 1.2.0</p>
         <p> <b>Subworkflow:</b> xxSubWorkflowxx</p>
         <p> <b> Maintainer:</b> jacob.karlstrom@med.lu.se</p>
         <p> <b>Description:</b> Your data has been processed by the nextflow pipeline singleCellWorkflows. If you want more information on how your data was processed, follow the link below and navigate to your release!</p>