From 0fedf6435a78da9afce4896e3456dce4cd5a93e5 Mon Sep 17 00:00:00 2001
From: deyazoubi <43732248+deyazoubi@users.noreply.github.com>
Date: Mon, 18 Nov 2019 15:04:45 +0100
Subject: [PATCH 1/3] 2nd round Sample sheet

---
 .../191009_SN737_0479_ACDU95ACXX_spike.csv    | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv

diff --git a/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv b/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
new file mode 100644
index 00000000..b9f9cc3f
--- /dev/null
+++ b/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
@@ -0,0 +1,56 @@
+[Header],,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,
+Date,10/09/19,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
+Description,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,
+Investigator,Ute Fischer/  Vera Jepsen ,,,,,,,,,,
+Backup_NAS_name,Ingerimm,,,,,,,,,,
+kind_of_run,2x101bp,,,,,,,,,,
+[Reads],,,,,,,,,,,
+101,,,,,,,,,,,
+101,,,,,,,,,,,
+,,,,,,,,,,,
+[Settings],,,,,,,,,,,
+ReverseComplement,0,,,,,,,,,,
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,,,
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,,,
+,,,,,,,,,,,
+[Data],,,,,,,,,,,
+Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,spike_entity_id,spike_entity_role,spike_ignore_sample
+1,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
+1,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430,healthy,
+1,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430,tumor,
+1,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
+2,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
+2,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430,healthy,
+2,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430,tumor,
+2,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
+3,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550,healthy,
+3,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550,tumor,
+3,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
+3,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765,healthy,
+4,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550,healthy,
+4,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550,tumor,
+4,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
+4,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765,healthy,
+5,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765,tumor,
+5,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
+5,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482,healthy,
+5,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482,tumor,
+6,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765,tumor,
+6,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
+6,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482,healthy,
+6,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482,tumor,
+7,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
+7,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565,healthy,
+7,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565,tumor,
+7,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,
+8,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
+8,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565,healthy,
+8,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565,tumor,
+8,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,

From 29fc9c4603d5f59e11b769dbd849a53cd58504e3 Mon Sep 17 00:00:00 2001
From: deyazoubi <43732248+deyazoubi@users.noreply.github.com>
Date: Fri, 29 Nov 2019 10:37:07 +0100
Subject: [PATCH 2/3] Delete 191009_SN737_0479_ACDU95ACXX_spike.csv

---
 .../191009_SN737_0479_ACDU95ACXX_spike.csv    | 56 -------------------
 1 file changed, 56 deletions(-)
 delete mode 100644 data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv

diff --git a/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv b/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
deleted file mode 100644
index b9f9cc3f..00000000
--- a/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
+++ /dev/null
@@ -1,56 +0,0 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,10/09/19,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Description,,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Investigator,Ute Fischer/  Vera Jepsen ,,,,,,,,,,
-Backup_NAS_name,Ingerimm,,,,,,,,,,
-kind_of_run,2x101bp,,,,,,,,,,
-[Reads],,,,,,,,,,,
-101,,,,,,,,,,,
-101,,,,,,,,,,,
-,,,,,,,,,,,
-[Settings],,,,,,,,,,,
-ReverseComplement,0,,,,,,,,,,
-Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,,,
-AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,,,
-,,,,,,,,,,,
-[Data],,,,,,,,,,,
-Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,spike_entity_id,spike_entity_role,spike_ignore_sample
-1,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
-1,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430,healthy,
-1,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430,tumor,
-1,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
-2,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
-2,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430,healthy,
-2,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430,tumor,
-2,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
-3,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550,healthy,
-3,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550,tumor,
-3,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
-3,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765,healthy,
-4,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550,healthy,
-4,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550,tumor,
-4,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
-4,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765,healthy,
-5,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765,tumor,
-5,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
-5,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482,healthy,
-5,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482,tumor,
-6,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765,tumor,
-6,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
-6,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482,healthy,
-6,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482,tumor,
-7,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
-7,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565,healthy,
-7,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565,tumor,
-7,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,
-8,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
-8,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565,healthy,
-8,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565,tumor,
-8,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,

From 3d1f39b4595b9c124b6fc7565dbbf56af34f1abe Mon Sep 17 00:00:00 2001
From: deyazoubi <43732248+deyazoubi@users.noreply.github.com>
Date: Fri, 29 Nov 2019 10:38:09 +0100
Subject: [PATCH 3/3] spike_entity_id

change spike_entity_id to distinguish between _rem and _rez
---
 .../191009_SN737_0479_ACDU95ACXX_spike.csv    | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv

diff --git a/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv b/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
new file mode 100644
index 00000000..7cd1c746
--- /dev/null
+++ b/data/samplesheets/191009_SN737_0479_ACDU95ACXX_spike.csv
@@ -0,0 +1,56 @@
+[Header],,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,
+Date,10/09/19,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
+Description,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,
+Investigator,Ute Fischer/  Vera Jepsen ,,,,,,,,,,
+Backup_NAS_name,Ingerimm,,,,,,,,,,
+kind_of_run,2x101bp,,,,,,,,,,
+[Reads],,,,,,,,,,,
+101,,,,,,,,,,,
+101,,,,,,,,,,,
+,,,,,,,,,,,
+[Settings],,,,,,,,,,,
+ReverseComplement,0,,,,,,,,,,
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,,,
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,,,
+,,,,,,,,,,,
+[Data],,,,,,,,,,,
+Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,spike_entity_id,spike_entity_role,spike_ignore_sample
+1,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
+1,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430_C2,healthy,
+1,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430_C2,tumor,
+1,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
+2,3430_ini,,,,A01,ATGCCTAA,ETV6_RUNX1,set1,3430,,
+2,3430_rem,,,,B01,GAATCTGA,ETV6_RUNX1,set1,3430_C2,healthy,
+2,3430_rez,,,,C01,AACGTGAT,ETV6_RUNX1,set1,3430_C2,tumor,
+2,2550_ini,,,,D01,CACTTCGA,ETV6_RUNX1,set1,2550,,
+3,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550_C2,healthy,
+3,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550_C2,tumor,
+3,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
+3,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765_C2,healthy,
+4,2550_rem,,,,E01,GCCAAGAC,ETV6_RUNX1,set2,2550_C2,healthy,
+4,2550_rez,,,,F01,GACTAGTA,ETV6_RUNX1,set2,2550_C2,tumor,
+4,2765_ini,,,,G01,ATTGGCTC,ETV6_RUNX1,set2,2765,,
+4,2765_rem,,,,H01,GATGAATC,ETV6_RUNX1,set2,2765_C2,healthy,
+5,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765_C2,tumor,
+5,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
+5,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482_C2,healthy,
+5,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482_C2,tumor,
+6,2765_rez,,,,A01,ATGCCTAA,ETV6_RUNX1,set3,2765_C2,tumor,
+6,3482_ini,,,,B01,GAATCTGA,ETV6_RUNX1,set3,3482,,
+6,3482_rem,,,,C01,AACGTGAT,ETV6_RUNX1,set3,3482_C2,healthy,
+6,3482_rez,,,,D01,CACTTCGA,ETV6_RUNX1,set3,3482_C2,tumor,
+7,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
+7,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565_C2,healthy,
+7,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565_C2,tumor,
+7,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,
+8,3565_ini,,,,E01,GCCAAGAC,ETV6_RUNX1,set4,3565,,
+8,3565_rem,,,,F01,GACTAGTA,ETV6_RUNX1,set4,3565_C2,healthy,
+8,3565_rez,,,,G01,ATTGGCTC,ETV6_RUNX1,set4,3565_C2,tumor,
+8,2578_ini,,,,H01,GATGAATC,ETV6_RUNX1,set4,2578,,