From c2585e3e60b1147474dff09404b330cceb42182d Mon Sep 17 00:00:00 2001
From: deyazoubi <43732248+deyazoubi@users.noreply.github.com>
Date: Fri, 17 Jan 2020 13:57:32 +0100
Subject: [PATCH 1/2] New sample sheet

case2
N T1
---
 .../191211_SN737_0487_BCDVUBACXX_spike.csv    | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv

diff --git a/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv b/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv
new file mode 100644
index 00000000..b8f4f960
--- /dev/null
+++ b/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv
@@ -0,0 +1,58 @@
+[Header],,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,
+Date,12/11/19,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,
+Investigator,Marina Oldenburg,,,,,,,,,,
+Application,HiSeq FASTQ,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
+Description,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,
+Operator,Daniel Scholtyssik,,,,,,,,,,
+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,mMYD_352_T,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_352,tumor,
+1,mMYD_353_N,,,,B02,GAGCTGAA,Maus_Hauer,,mMYD_353,healthy,
+1,mMYD_353_T,,,,C02,AAACATCG,Maus_Hauer,,mMYD_353,tumor,
+1,mMYD_354_N,,,,D02,GAGTTAGC,Maus_Hauer,,MMYD_354,healthy,
+2,mMYD_354_T,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_354,tumor,
+2,mNU_362_N,,,,B02,GAGCTGAA,Maus_Hauer,,MNU_362,healthy,
+2,mNU_362_T,,,,C02,AAACATCG,Maus_Hauer,,MNU_362,tumor,
+2,mRJ_366_N,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_366,healthy,
+3,mRJ_366_T1,,,,A02,AGCAGGAA,Maus_Hauer,,MRJ_366,tumor,
+3,mRJ_366_T2,,,,B02,GAGCTGAA,Maus_Hauer,,mRJ_366_C2,,
+3,mCD_367_N,,,,C02,AAACATCG,Maus_Hauer,,MCD_367,healthy,
+3,mCD_367_T,,,,D02,GAGTTAGC,Maus_Hauer,,MCD_367,tumor,
+4,mMYD_370_N,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_370,healthy,
+4,mMYD_370_T,,,,B02,GAGCTGAA,Maus_Hauer,,MMYD_370,tumor,
+4,mMYD_371_N,,,,C02,AAACATCG,Maus_Hauer,,MMYD_371,healthy,
+4,mMYD_371_T,,,,D02,GAGTTAGC,Maus_Hauer,,MMYD_371,tumor,
+5,mMYD_372_N,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_372,healthy,
+5,mMYD_372_T,,,,B02,GAGCTGAA,Maus_Hauer,,MMYD_372,tumor,
+5,mMYD_373_N,,,,C02,AAACATCG,Maus_Hauer,,MMYD_373,healthy,
+5,mMYD_373_T,,,,D02,GAGTTAGC,Maus_Hauer,,MMYD_373,tumor,
+6,mMYD_376_N,,,,E02,CGAACTTA,Maus_Hauer,,MMYD_376,healthy,
+6,mMYD_376_T,,,,F02,GATAGACA,Maus_Hauer,,MMYD_376,tumor,
+6,mMYD_377_N,,,,G02,AAGGACAC,Maus_Hauer,,MMYD_377,healthy,
+6,mMYD_377_T,,,,H02,GACAGTGC,Maus_Hauer,,MMYD_377,tumor,
+6,mRJ_381_T2,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381_C2,,
+7,mCD_378_N,,,,A02,AGCAGGAA,Maus_Hauer,,MCD_378,healthy,
+7,mCD_378_T,,,,B02,GAGCTGAA,Maus_Hauer,,MCD_378,tumor,
+7,mAB_379_N,,,,C02,AAACATCG,Maus_Hauer,,MAB_379,healthy,
+7,mAB_379_T,,,,D02,GAGTTAGC,Maus_Hauer,,MAB_379,tumor,
+8,mRJ_380_N,,,,A02,AGCAGGAA,Maus_Hauer,,MRJ_380,healthy,
+8,mRJ_380_T1,,,,B02,GAGCTGAA,Maus_Hauer,,MRJ_380,tumor,
+8,mRJ_381_N,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381,healthy,
+8,mRJ_381_T1,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_381,tumor,

From 80d7db6b7eda0b5df4f11b7d1eca12b27fe459a0 Mon Sep 17 00:00:00 2001
From: deyazoubi <43732248+deyazoubi@users.noreply.github.com>
Date: Wed, 29 Jan 2020 11:58:03 +0100
Subject: [PATCH 2/2] case 2

healthy with tumor T2
---
 .../191211_SN737_0487_BCDVUBACXX_spike.csv           | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv b/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv
index b8f4f960..ca3ac831 100644
--- a/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv
+++ b/data/samplesheets/191211_SN737_0487_BCDVUBACXX_spike.csv
@@ -30,9 +30,9 @@ Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Pro
 2,mMYD_354_T,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_354,tumor,
 2,mNU_362_N,,,,B02,GAGCTGAA,Maus_Hauer,,MNU_362,healthy,
 2,mNU_362_T,,,,C02,AAACATCG,Maus_Hauer,,MNU_362,tumor,
-2,mRJ_366_N,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_366,healthy,
-3,mRJ_366_T1,,,,A02,AGCAGGAA,Maus_Hauer,,MRJ_366,tumor,
-3,mRJ_366_T2,,,,B02,GAGCTGAA,Maus_Hauer,,mRJ_366_C2,,
+2,mRJ_366_N,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_366_C2,healthy,
+3,mRJ_366_T1,,,,A02,AGCAGGAA,Maus_Hauer,,MRJ_366,,
+3,mRJ_366_T2,,,,B02,GAGCTGAA,Maus_Hauer,,MRJ_366_C2,tumor,
 3,mCD_367_N,,,,C02,AAACATCG,Maus_Hauer,,MCD_367,healthy,
 3,mCD_367_T,,,,D02,GAGTTAGC,Maus_Hauer,,MCD_367,tumor,
 4,mMYD_370_N,,,,A02,AGCAGGAA,Maus_Hauer,,MMYD_370,healthy,
@@ -47,12 +47,12 @@ Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Pro
 6,mMYD_376_T,,,,F02,GATAGACA,Maus_Hauer,,MMYD_376,tumor,
 6,mMYD_377_N,,,,G02,AAGGACAC,Maus_Hauer,,MMYD_377,healthy,
 6,mMYD_377_T,,,,H02,GACAGTGC,Maus_Hauer,,MMYD_377,tumor,
-6,mRJ_381_T2,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381_C2,,
+6,mRJ_381_T2,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381_C2,tumor,
 7,mCD_378_N,,,,A02,AGCAGGAA,Maus_Hauer,,MCD_378,healthy,
 7,mCD_378_T,,,,B02,GAGCTGAA,Maus_Hauer,,MCD_378,tumor,
 7,mAB_379_N,,,,C02,AAACATCG,Maus_Hauer,,MAB_379,healthy,
 7,mAB_379_T,,,,D02,GAGTTAGC,Maus_Hauer,,MAB_379,tumor,
 8,mRJ_380_N,,,,A02,AGCAGGAA,Maus_Hauer,,MRJ_380,healthy,
 8,mRJ_380_T1,,,,B02,GAGCTGAA,Maus_Hauer,,MRJ_380,tumor,
-8,mRJ_381_N,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381,healthy,
-8,mRJ_381_T1,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_381,tumor,
+8,mRJ_381_N,,,,C02,AAACATCG,Maus_Hauer,,MRJ_381_C2,healthy,
+8,mRJ_381_T1,,,,D02,GAGTTAGC,Maus_Hauer,,MRJ_381,,