diff --git a/data/samplesheets/131015_SN737_0288_AD287JACXX_spike.csv b/data/samplesheets/131015_SN737_0288_AD287JACXX_spike.csv
index 90fd3c84..96fc8301 100644
--- a/data/samplesheets/131015_SN737_0288_AD287JACXX_spike.csv
+++ b/data/samplesheets/131015_SN737_0288_AD287JACXX_spike.csv
@@ -1,47 +1,47 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,10/15/13,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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
-1,514_rez2,,,,Index_4,TGACCA,Inform,,,,
-1,514_rez_pSCT,,,,Index_6,GCCAAT,Inform,,,,
-1,514_rem,,,,Index_12,CTTGTA,Inform,,,,
-2,514_pSCT,,,,Index_4,TGACCA,Inform,,,,
-2,514_ini,,,,Index_6,GCCAAT,Inform,,,,
-2,514_ini2,,,,Index_12,CTTGTA,Inform,,,,
-3,590_rez,,,,Index_4,TGACCA,Inform,,,,
-3,590_rez_pSCT,,,,Index_6,GCCAAT,Inform,,,,
-3,590_rem,,,,Index_12,CTTGTA,Inform,,,,
-4,590_DONOR,,,,Index_6,GCCAAT,Inform,,,,
-4,590_pSCT,,,,Index_12,CTTGTA,Inform,,,,
-4,660_rez,,,,Index_4,TGACCA,Inform,,,,
-5,660_rez_pSCT,,,,Index_4,TGACCA,Inform,,,,
-5,660_rem,,,,Index_6,GCCAAT,Inform,,,,
-5,660_pSCT,,,,Index_12,CTTGTA,Inform,,,,
-6,685_rez,,,,Index_4,TGACCA,Inform,,,,
-6,685_rez_pSCT,,,,Index_6,GCCAAT,Inform,,,,
-6,735_rez,,,,Index_12,CTTGTA,Inform,,,,
-7,685_pSCT,,,,Index_4,TGACCA,Inform,,,,
-7,707_rez,,,,Index_6,GCCAAT,Inform,,,,
-7,707_rez_pSCT,,,,Index_12,CTTGTA,Inform,,,,
-8,707_rem,,,,Index_4,TGACCA,Inform,,,,
-8,685_rem,,,,Index_6,GCCAAT,Inform,,,,
-8,735_rez_pSCT,,,,Index_12,CTTGTA,Inform,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,10/15/13,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+2,514_INIT,,,,Index_6,GCCAAT,Inform,,514,,,514_ini
+2,514_INIT_B,,,,Index_12,CTTGTA,Inform,,514,,,514_ini2
+2,514_TREMI,,,,Index_4,TGACCA,Inform,,514,,,514_pSCT
+1,514_REMI,,,,Index_12,CTTGTA,Inform,,514,,,514_rem
+1,514_TRLPS,,,,Index_6,GCCAAT,Inform,,514,,,514_rez_pSCT
+1,514_RLPS,,,,Index_4,TGACCA,Inform,,514,,,514_rez2
+4,590_TRANS,,,,Index_6,GCCAAT,Inform,,590,,,590_DONOR
+4,590_TREMI,,,,Index_12,CTTGTA,Inform,,590,,,590_pSCT
+3,590_REMI,,,,Index_12,CTTGTA,Inform,,590,,,590_rem
+3,590_RLPS,,,,Index_4,TGACCA,Inform,,590,,,590_rez
+3,590_TRLPS,,,,Index_6,GCCAAT,Inform,,590,,,590_rez_pSCT
+5,660_TREMI,,,,Index_12,CTTGTA,Inform,,660,,,660_pSCT
+5,660_rem,,,,Index_6,GCCAAT,Inform,,,,,
+4,660_RLPS,,,,Index_4,TGACCA,Inform,,660,,,660_rez
+5,660_TRLPS,,,,Index_4,TGACCA,Inform,,660,,,660_rez_pSCT
+7,685_pSCT,,,,Index_4,TGACCA,Inform,,,,,
+8,685_rem,,,,Index_6,GCCAAT,Inform,,,,,
+6,685_rez,,,,Index_4,TGACCA,Inform,,,,,
+6,685_rez_pSCT,,,,Index_6,GCCAAT,Inform,,,,,
+8,707_REMI,,,,Index_4,TGACCA,Inform,,707,,,707_rem
+7,707_rez,,,,Index_6,GCCAAT,Inform,,,,,
+7,707_TRLPS,,,,Index_12,CTTGTA,Inform,,707,,,707_rez_pSCT
+6,735_RLPS,,,,Index_12,CTTGTA,Inform,,735,,,735_rez
+8,735_rez_pSCT,,,,Index_12,CTTGTA,Inform,,,,,
diff --git a/data/samplesheets/140128_SN737_0297_AD2HGUACXX_spike.csv b/data/samplesheets/140128_SN737_0297_AD2HGUACXX_spike.csv
index 910259f0..ae09904f 100644
--- a/data/samplesheets/140128_SN737_0297_AD2HGUACXX_spike.csv
+++ b/data/samplesheets/140128_SN737_0297_AD2HGUACXX_spike.csv
@@ -1,47 +1,47 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,01/28/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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,AT1_tumor,,,,Index_4,TGACCA,AT_NBS,,,,
-1,AT1_healthy,,,,Index_6,GCCAAT,AT_NBS,,,,
-1,AT2_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,
-2,AT2_healthy,,,,Index_4,TGACCA,AT_NBS,,,,
-2,NBS_1_tumor,,,,Index_6,GCCAAT,AT_NBS,,,,
-2,NBS_1_healthy,,,,Index_12,CTTGTA,AT_NBS,,,,
-3,NBS_2_tumor,,,,Index_4,TGACCA,AT_NBS,,,,
-3,NBS_2_healthy,,,,Index_6,GCCAAT,AT_NBS,,,,
-3,NBS_3_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,
-4,Sa_Do_MNC_7,,,,Index_4,TGACCA,Dohle,,,,
-4,Sa_Do_MNC_27_rem,,,,Index_6,GCCAAT,Dohle,,,,
-4,Alps_21,,,,Index_12,CTTGTA,Schafiq,,,,
-5,HV171,,,,Index_4,TGACCA,INFORM,,,,
-5,ALPS_17,,,,Index_6,GCCAAT,Alps,,ALPS_17,patient,
-5,ALPS_18,,,,Index_12,CTTGTA,Alps,,ALPS_18,patient,
-6,17870,,,,Index_4,TGACCA,INFORM,,,,
-6,90127,,,,Index_6,GCCAAT,INFORM,,,,
-6,KA28,,,,Index_12,CTTGTA,INFORM,,,,
-7,60101,,,,Index_4,TGACCA,INFORM,,,,
-7,60210,,,,Index_6,GCCAAT,INFORM,,,,
-7,KA28,,,,Index_12,CTTGTA,INFORM,,,,
-8,17463,,,,Index_4,TGACCA,INFORM,,,,
-8,17763,,,,Index_6,GCCAAT,INFORM,,,,
-8,NBS_3_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,01/28/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+1,AT1_tumor,,,,Index_4,TGACCA,AT_NBS,,,,,
+1,AT1_healthy,,,,Index_6,GCCAAT,AT_NBS,,,,,
+1,AT2_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,,
+2,AT2_healthy,,,,Index_4,TGACCA,AT_NBS,,,,,
+2,NBS_1_tumor,,,,Index_6,GCCAAT,AT_NBS,,,,,
+2,NBS_1_healthy,,,,Index_12,CTTGTA,AT_NBS,,,,,
+3,NBS_2_tumor,,,,Index_4,TGACCA,AT_NBS,,,,,
+3,NBS_2_healthy,,,,Index_6,GCCAAT,AT_NBS,,,,,
+3,NBS_3_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,,
+4,Sa_Do_MNC_7,,,,Index_4,TGACCA,Dohle,,,,,
+4,Sa_Do_MNC_27_rem,,,,Index_6,GCCAAT,Dohle,,,,,
+4,Alps_21,,,,Index_12,CTTGTA,Schafiq,,,,,
+5,685_INIT,,,,Index_4,TGACCA,Inform,,685,,,HV171
+5,ALPS_17,,,,Index_6,GCCAAT,Alps,,ALPS_17,patient,,
+5,ALPS_18,,,,Index_12,CTTGTA,Alps,,ALPS_18,patient,,
+6,735_TRLPS,,,,Index_4,TGACCA,Inform,,735,,,17870
+6,90127,,,,Index_6,GCCAAT,Inform,,,,,
+6,590_INIT,,,,Index_12,CTTGTA,Inform,,590,,,KA28
+7,60101,,,,Index_4,TGACCA,Inform,,,,,
+7,60210,,,,Index_6,GCCAAT,Inform,,,,,
+7,590_INIT,,,,Index_12,CTTGTA,Inform,,590,,,KA28
+8,735_REMI,,,,Index_4,TGACCA,Inform,,735,,,17463
+8,735_TREMI,,,,Index_6,GCCAAT,Inform,,735,,,17763
+8,NBS_3_tumor,,,,Index_12,CTTGTA,AT_NBS,,,,,
diff --git a/data/samplesheets/140306_SN737_0303_AC3FLHACXX_spike.csv b/data/samplesheets/140306_SN737_0303_AC3FLHACXX_spike.csv
index fa73060f..7b78aa3c 100644
--- a/data/samplesheets/140306_SN737_0303_AC3FLHACXX_spike.csv
+++ b/data/samplesheets/140306_SN737_0303_AC3FLHACXX_spike.csv
@@ -1,48 +1,48 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,03/06/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Investigator,Ute Fischer,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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
-1,1_T,,,,Index_4,TGACCA,Maus_Hauer,,1,tumor,
-1,1_C,,,,Index_6,GCCAAT,Maus_Hauer,,1,healthy,
-1,2_T,,,,Index_12,CTTGTA,Maus_Hauer,,2,tumor,
-2,2_C,,,,Index_4,TGACCA,Maus_Hauer,,2,healthy,
-2,3_T,,,,Index_6,GCCAAT,Maus_Hauer,,3,tumor,
-2,3_C,,,,Index_12,CTTGTA,Maus_Hauer,,3,healthy,
-3,4_T,,,,Index_4,TGACCA,Maus_Hauer,,4,tumor,
-3,4_C,,,,Index_6,GCCAAT,Maus_Hauer,,4,healthy,
-3,5_T,,,,Index_12,CTTGTA,Maus_Hauer,,5,tumor,
-4,5_C,,,,Index_4,TGACCA,Maus_Hauer,,5,healthy,
-4,6_T,,,,Index_6,GCCAAT,Maus_Hauer,,6,tumor,
-4,6_C,,,,Index_12,CTTGTA,Maus_Hauer,,6,healthy,
-5,7_T,,,,Index_4,TGACCA,Maus_Hauer,,7,tumor,
-5,7_C,,,,Index_6,GCCAAT,Maus_Hauer,,7,healthy,
-5,8_T,,,,Index_12,CTTGTA,Maus_Hauer,,8,tumor,
-6,8_C,,,,Index_4,TGACCA,Maus_Hauer,,8,healthy,
-6,9_T,,,,Index_6,GCCAAT,Maus_Hauer,,9_303,tumor,
-6,9_C,,,,Index_12,CTTGTA,Maus_Hauer,,9_303,healthy,
-7,10_T,,,,Index_4,TGACCA,Maus_Hauer,,10,tumor,
-7,17424,,,,Index_6,GCCAAT,INFORM,,,,
-7,10_C,,,,Index_12,CTTGTA,Maus_Hauer,,10,healthy,
-8,11_T,,,,Index_4,TGACCA,Maus_Hauer,,11,tumor,
-8,17034,,,,Index_6,GCCAAT,INFORM,,,,
-8,11_C,,,,Index_12,CTTGTA,Maus_Hauer,,11,healthy,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,03/06/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Investigator,Ute Fischer,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+1,1_T,,,,Index_4,TGACCA,Maus_Hauer,,1,tumor,,
+1,1_C,,,,Index_6,GCCAAT,Maus_Hauer,,1,healthy,,
+1,2_T,,,,Index_12,CTTGTA,Maus_Hauer,,2,tumor,,
+2,2_C,,,,Index_4,TGACCA,Maus_Hauer,,2,healthy,,
+2,3_T,,,,Index_6,GCCAAT,Maus_Hauer,,3,tumor,,
+2,3_C,,,,Index_12,CTTGTA,Maus_Hauer,,3,healthy,,
+3,4_T,,,,Index_4,TGACCA,Maus_Hauer,,4,tumor,,
+3,4_C,,,,Index_6,GCCAAT,Maus_Hauer,,4,healthy,,
+3,5_T,,,,Index_12,CTTGTA,Maus_Hauer,,5,tumor,,
+4,5_C,,,,Index_4,TGACCA,Maus_Hauer,,5,healthy,,
+4,6_T,,,,Index_6,GCCAAT,Maus_Hauer,,6,tumor,,
+4,6_C,,,,Index_12,CTTGTA,Maus_Hauer,,6,healthy,,
+5,7_T,,,,Index_4,TGACCA,Maus_Hauer,,7,tumor,,
+5,7_C,,,,Index_6,GCCAAT,Maus_Hauer,,7,healthy,,
+5,8_T,,,,Index_12,CTTGTA,Maus_Hauer,,8,tumor,,
+6,8_C,,,,Index_4,TGACCA,Maus_Hauer,,8,healthy,,
+6,9_T,,,,Index_6,GCCAAT,Maus_Hauer,,9_303,tumor,,
+6,9_C,,,,Index_12,CTTGTA,Maus_Hauer,,9_303,healthy,,
+7,10_T,,,,Index_4,TGACCA,Maus_Hauer,,10,tumor,,
+7,685_TRLPS,,,,Index_6,GCCAAT,Inform,,685,,,17424
+7,10_C,,,,Index_12,CTTGTA,Maus_Hauer,,10,healthy,,
+8,11_T,,,,Index_4,TGACCA,Maus_Hauer,,11,tumor,,
+8,685_REMI,,,,Index_6,GCCAAT,Inform,,685,,,17034
+8,11_C,,,,Index_12,CTTGTA,Maus_Hauer,,11,healthy,,
diff --git a/data/samplesheets/140318_SN737_0304_AC41UTACXX_spike.csv b/data/samplesheets/140318_SN737_0304_AC41UTACXX_spike.csv
index a46a408d..4ec75fd0 100755
--- a/data/samplesheets/140318_SN737_0304_AC41UTACXX_spike.csv
+++ b/data/samplesheets/140318_SN737_0304_AC41UTACXX_spike.csv
@@ -1,49 +1,49 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,03/18/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Investigator,DKTK,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-kind_of_run,2x101bp,,,,,,,,,,
-Notes,AML_m_14_ini_typo in samplesheet/is an initial 30ng,,,,,,,,,,
-[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,brain_skin_w_1,,,,,TGACCA,Hoell,,,,
-1,brain_skin_m_2,,,,,GCCAAT,Hoell,,,,
-1,brain_skin_m_3,,,,,CTTGTA,Hoell,,,,
-2,brain_skin_m_4,,,,,TGACCA,Hoell,,,,
-2,brain_skin_w_5,,,,,GCCAAT,Hoell,,,,
-2,1_LCL_wt_EBV,,,,,CTTGTA,AB_MUC_cells,,,,
-3,2_LCL_wt_EBV,,,,,TGACCA,AB_MUC_cells,,,,
-3,3_EBNA3C_def_LCLs,,,,,GCCAAT,AB_MUC_cells,,,,
-3,4_EBNA3C_def_LCLs,,,,,CTTGTA,AB_MUC_cells,,,,
-4,StA_BS,,,,,TGACCA,AT_StA,,,,
-4,StA_SS,,,,,GCCAAT,AT_StA,,,,
-4,StA_ES,,,,,CTTGTA,AT_StA,,,,
-5,UKDEBV_201P,,,,,TGACCA,UKDEBV,,,,
-5,UKDEBV_201B,,,,,GCCAAT,UKDEBV,,,,
-5,UKDEBV_201M,,,,,CTTGTA,UKDEBV,,,,
-6,UKDEBV_201F,,,,,TGACCA,UKDEBV,,,,
-6,AML_m_20_initial,,,,,GCCAAT,DKTK,,,,
-6,ALPS_22,,,,,CTTGTA,Alps,,ALPS_22,patient,
-7,AML_m_14_inititial,,,,,TGACCA,DKTK,,,,
-7,AML_m_25_remission,,,,,GCCAAT,DKTK,,,,
-7,AML_m_25_initial,,,,,CTTGTA,DKTK,,,,
-8,A198_TALL,,,,,TGACCA,Fischer,,,,
-8,A198_Remission,,,,,GCCAAT,Fischer,,,,
-8,M248,,,,,CTTGTA,INFORM,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,03/18/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Investigator,DKTK,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+kind_of_run,2x101bp,,,,,,,,,,,
+Notes,AML_m_14_ini_typo in samplesheet/is an initial 30ng,,,,,,,,,,,
+[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,spike_original_but_wrong_sample_id
+1,brain_skin_w_1,,,,,TGACCA,Hoell,,,,,
+1,brain_skin_m_2,,,,,GCCAAT,Hoell,,,,,
+1,brain_skin_m_3,,,,,CTTGTA,Hoell,,,,,
+2,brain_skin_m_4,,,,,TGACCA,Hoell,,,,,
+2,brain_skin_w_5,,,,,GCCAAT,Hoell,,,,,
+2,1_LCL_wt_EBV,,,,,CTTGTA,AB_MUC_cells,,,,,
+3,2_LCL_wt_EBV,,,,,TGACCA,AB_MUC_cells,,,,,
+3,3_EBNA3C_def_LCLs,,,,,GCCAAT,AB_MUC_cells,,,,,
+3,4_EBNA3C_def_LCLs,,,,,CTTGTA,AB_MUC_cells,,,,,
+4,StA_BS,,,,,TGACCA,AT_StA,,,,,
+4,StA_SS,,,,,GCCAAT,AT_StA,,,,,
+4,StA_ES,,,,,CTTGTA,AT_StA,,,,,
+5,UKDEBV_201P,,,,,TGACCA,UKDEBV,,,,,
+5,UKDEBV_201B,,,,,GCCAAT,UKDEBV,,,,,
+5,UKDEBV_201M,,,,,CTTGTA,UKDEBV,,,,,
+6,UKDEBV_201F,,,,,TGACCA,UKDEBV,,,,,
+6,AML_m_20_initial,,,,,GCCAAT,DKTK,,,,,
+6,ALPS_22,,,,,CTTGTA,Alps,,ALPS_22,patient,,
+7,AML_m_14_inititial,,,,,TGACCA,DKTK,,,,,
+7,AML_m_25_remission,,,,,GCCAAT,DKTK,,,,,
+7,AML_m_25_initial,,,,,CTTGTA,DKTK,,,,,
+8,A198_TALL,,,,,TGACCA,Fischer,,,,,
+8,A198_Remission,,,,,GCCAAT,Fischer,,,,,
+8,660_INIT,,,,,CTTGTA,Inform,,660,,,M248
diff --git a/data/samplesheets/140616_SN737_0307_AC2PFCACXX_spike.csv b/data/samplesheets/140616_SN737_0307_AC2PFCACXX_spike.csv
index 0fb557ff..036ad093 100644
--- a/data/samplesheets/140616_SN737_0307_AC2PFCACXX_spike.csv
+++ b/data/samplesheets/140616_SN737_0307_AC2PFCACXX_spike.csv
@@ -1,49 +1,49 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,06/16/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Investigator,Pablo Landgraf/Ute Fischer/Sujal Ghosh/Andrea Hoenscheid/Shai Izraeli/Roland Meisel,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-kind_of_run,2x101bp,,,,,,,,,,
-Notes,3h no power cyc 133/imaging/restarted/data integrated from temp,,,,,,,,,,
-[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
-1,1557,,,,Index_4,TGACCA,Ufoplan,,,,
-1,1402,,,,Index_6,GCCAAT,Ufoplan,,,,
-1,A198_T_All_4451,,,,Index_12,CTTGTA,T_ALL_T_LBL_Hauer_Fischer,,,,
-2,AML_m_14_initial,,,,Index_4,TGACCA,DKTK,,,,
-2,16729,,,,Index_6,GCCAAT,Inform,,,,
-2,1405,,,,Index_12,CTTGTA,Ufoplan,,,,
-3,P007_initial,,,,Index_4,TGACCA,Sujal,,,,
-3,P007_remission,,,,Index_6,GCCAAT,Sujal,,,,
-3,P007_recurrence,,,,Index_12,CTTGTA,Sujal,,,,
-4,UKDID_17P,,,,Index_4,TGACCA,UKDID,,UKDID_17,,
-4,UKDID_17F1,,,,Index_6,GCCAAT,UKDID,,UKDID_17,,
-4,UKDID_17F2,,,,Index_12,CTTGTA,UKDID,,UKDID_17,,
-5,UKDID_17S,,,,Index_4,TGACCA,UKDID,,UKDID_17,,
-5,A410_ALL_3142,,,,Index_6,GCCAAT,dsALL,,A410,,
-5,A410_remission_4220,,,,Index_12,CTTGTA,dsALL,,A410,,
-6,AML_m_22_remission,,,,Index_4,TGACCA,DKTK,,,,
-6,AML_m_22_initial,,,,Index_6,GCCAAT,DKTK,,,,
-6,AML_w_24_remission,,,,Index_12,CTTGTA,DKTK,,,,
-7,AML_w_24_initial,,,,Index_4,TGACCA,DKTK,,,,
-7,AML_m_32_remission,,,,Index_6,GCCAAT,DKTK,,,,
-7,AML_m_32_initial,,,,Index_12,CTTGTA,DKTK,,,,
-8,16828,,,,Index_4,TGACCA,Inform,,,,
-8,17221,,,,Index_6,GCCAAT,Inform,,,,
-8,16695,,,,Index_12,CTTGTA,Inform,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,06/16/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Investigator,Pablo Landgraf/Ute Fischer/Sujal Ghosh/Andrea Hoenscheid/Shai Izraeli/Roland Meisel,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+kind_of_run,2x101bp,,,,,,,,,,,
+Notes,3h no power cyc 133/imaging/restarted/data integrated from temp,,,,,,,,,,,
+[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,spike_original_but_wrong_sample_id
+1,1557,,,,Index_4,TGACCA,Ufoplan,,,,,
+1,1402,,,,Index_6,GCCAAT,Ufoplan,,,,,
+1,A198_T_All_4451,,,,Index_12,CTTGTA,T_ALL_T_LBL_Hauer_Fischer,,,,,
+2,AML_m_14_initial,,,,Index_4,TGACCA,DKTK,,,,,
+2,660_rem,,,,Index_6,GCCAAT,Inform,,660,,,16729
+2,1405,,,,Index_12,CTTGTA,Ufoplan,,,,,
+3,P007_initial,,,,Index_4,TGACCA,Sujal,,,,,
+3,P007_remission,,,,Index_6,GCCAAT,Sujal,,,,,
+3,P007_recurrence,,,,Index_12,CTTGTA,Sujal,,,,,
+4,UKDID_17P,,,,Index_4,TGACCA,UKDID,,UKDID_17,,,
+4,UKDID_17F1,,,,Index_6,GCCAAT,UKDID,,UKDID_17,,,
+4,UKDID_17F2,,,,Index_12,CTTGTA,UKDID,,UKDID_17,,,
+5,UKDID_17S,,,,Index_4,TGACCA,UKDID,,UKDID_17,,,
+5,A410_ALL_3142,,,,Index_6,GCCAAT,dsALL,,A410,,,
+5,A410_remission_4220,,,,Index_12,CTTGTA,dsALL,,A410,,,
+6,AML_m_22_remission,,,,Index_4,TGACCA,DKTK,,,,,
+6,AML_m_22_initial,,,,Index_6,GCCAAT,DKTK,,,,,
+6,AML_w_24_remission,,,,Index_12,CTTGTA,DKTK,,,,,
+7,AML_w_24_initial,,,,Index_4,TGACCA,DKTK,,,,,
+7,AML_m_32_remission,,,,Index_6,GCCAAT,DKTK,,,,,
+7,AML_m_32_initial,,,,Index_12,CTTGTA,DKTK,,,,,
+8,685_RLPS,,,,Index_4,TGACCA,Inform,,685,,,16828
+8,685_TREMI,,,,Index_6,GCCAAT,Inform,,685,,,17221
+8,707_RLPS,,,,Index_12,CTTGTA,Inform,,707,,,16695
diff --git a/data/samplesheets/140814_SN737_0323_AC42J8ACXX_spike.csv b/data/samplesheets/140814_SN737_0323_AC42J8ACXX_spike.csv
index 3e05a0e1..bc2bc0ec 100644
--- a/data/samplesheets/140814_SN737_0323_AC42J8ACXX_spike.csv
+++ b/data/samplesheets/140814_SN737_0323_AC42J8ACXX_spike.csv
@@ -1,95 +1,95 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,08/14/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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,Reti_MNC_7,,,,Index_1,ATCACG,MSC,,,,
-1,ALPS_54,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_54,patient,
-1,Reti_MSC_7,,,,Index_5,ACAGTG,MSC,,,,
-1,ALPS_55,,,,Index_6,GCCAAT,Alps,,Ulm_ALPS_55,patient,
-1,Reti_MNCplus39_remi,,,,Index_8,ACTTGA,MSC,,,,
-1,Reti_Fibros,,,,Index_10,TAGCTT,MSC,,,,
-1,ALPS_548,,,,Index_12,CTTGTA,Alps,,Ulm_ALPS_548,patient,
-1,R_7_1,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-1,F_9T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-2,Reti_MNC_7,,,,Index_1,ATCACG,MSC,,,,
-2,ALPS_54,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_54,patient,
-2,Reti_MSC_7,,,,Index_5,ACAGTG,MSC,,,,
-2,ALPS_55,,,,Index_6,GCCAAT,Alps,,Ulm_ALPS_55,patient,
-2,Reti_MNCplus39_remi,,,,Index_8,ACTTGA,MSC,,,,
-2,Reti_Fibros,,,,Index_10,TAGCTT,MSC,,,,
-2,ALPS_548,,,,Index_12,CTTGTA,Alps,,Ulm_ALPS_548,patient,
-2,R_7_2,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-2,F_10T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-3,Herka_MNC_7,,,,Index_1,ATCACG,MSC,,,,
-3,ALPS_549,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_549,patient,
-3,Herka_MSC_7,,,,Index_5,ACAGTG,MSC,,,,
-3,Herka_MNCplus51_Remi,,,,Index_6,GCCAAT,MSC,,,,
-3,Herka_Fibros,,,,Index_8,ACTTGA,MSC,,,,
-3,Dewo_MNC_7,,,,Index_10,TAGCTT,MSC,,,,
-3,Dewo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,
-3,R_7_3,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-3,F_11T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-4,Herka_MNC_7,,,,Index_1,ATCACG,MSC,,,,
-4,ALPS_549,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_549,patient,
-4,Herka_MSC_7,,,,Index_5,ACAGTG,MSC,,,,
-4,Herka_MNCplus51_Remi,,,,Index_6,GCCAAT,MSC,,,,
-4,Herka_Fibros,,,,Index_8,ACTTGA,MSC,,,,
-4,Dewo_MNC_7,,,,Index_10,TAGCTT,MSC,,,,
-4,Dewo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,
-4,R_7_4,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-4,F_12T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-5,Dewo_MNCplus51_Remi,,,,Index_1,ATCACG,MSC,,,,
-5,Dewo_Fibros,,,,Index_4,TGACCA,MSC,,,,
-5,P_AML_Bulk_MNC,,,,Index_5,ACAGTG,MSC,,,,
-5,14_0291,,,,Index_6,GCCAAT,Humangenetik_Wien,,,,
-5,P_AML_CD34plus_CD41,,,,Index_8,ACTTGA,MSC,,,,
-5,20202,,,,Index_10,TAGCTT,Infom_Meisel,,,,
-5,14_0152,,,,Index_12,CTTGTA,Humangenetik_Wien,,,,
-5,R_7_5,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-5,F_13T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-6,Dewo_MNCplus51_Remi,,,,Index_1,ATCACG,MSC,,,,
-6,Dewo_Fibros,,,,Index_4,TGACCA,MSC,,,,
-6,P_AML_Bulk_MNC,,,,Index_5,ACAGTG,MSC,,,,
-6,14_0291,,,,Index_6,GCCAAT,Humangenetik_Wien,,,,
-6,P_AML_CD34plus_CD41,,,,Index_8,ACTTGA,MSC,,,,
-6,20202,,,,Index_10,TAGCTT,Infom_Meisel,,,,
-6,14_0152,,,,Index_12,CTTGTA,Humangenetik_Wien,,,,
-6,R_7_6,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-6,F_37T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-7,19635,,,,Index_1,ATCACG,Infom_Meisel,,,,
-7,14_0174,,,,Index_4,TGACCA,Humangenetik_Wien,,,,
-7,Rova_MNC_7,,,,Index_5,ACAGTG,MSC,,,,
-7,Rova_MSC_7,,,,Index_6,GCCAAT,MSC,,,,
-7,Rova_MSCplus41_Remi,,,,Index_8,ACTTGA,MSC,,,,
-7,Rova_Fibtos,,,,Index_10,TAGCTT,MSC,,,,
-7,Azem_MNC_7,,,,Index_12,CTTGTA,MSC,,,,
-7,R_7_8,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-7,F_44T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
-8,19635,,,,Index_1,ATCACG,Infom_Meisel,,,,
-8,14_0174,,,,Index_4,TGACCA,Humangenetik_Wien,,,,
-8,Rova_MNC_7,,,,Index_5,ACAGTG,MSC,,,,
-8,Rova_MSC_7,,,,Index_6,GCCAAT,MSC,,,,
-8,Rova_MSCplus41_Remi,,,,Index_8,ACTTGA,MSC,,,,
-8,Rova_Fibtos,,,,Index_10,TAGCTT,MSC,,,,
-8,Azem_MNC_7,,,,Index_12,CTTGTA,MSC,,,,
-8,R_7_10,,,,Index_7,CAGATC,Amplicon_Rene,,,,
-8,F_49T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,08/14/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+1,Reti_MNC_7,,,,Index_1,ATCACG,MSC,,,,,
+1,ALPS_54,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_54,patient,,
+1,Reti_MSC_7,,,,Index_5,ACAGTG,MSC,,,,,
+1,ALPS_55,,,,Index_6,GCCAAT,Alps,,Ulm_ALPS_55,patient,,
+1,Reti_MNCplus39_remi,,,,Index_8,ACTTGA,MSC,,,,,
+1,Reti_Fibros,,,,Index_10,TAGCTT,MSC,,,,,
+1,ALPS_548,,,,Index_12,CTTGTA,Alps,,Ulm_ALPS_548,patient,,
+1,R_7_1,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+1,F_9T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+2,Reti_MNC_7,,,,Index_1,ATCACG,MSC,,,,,
+2,ALPS_54,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_54,patient,,
+2,Reti_MSC_7,,,,Index_5,ACAGTG,MSC,,,,,
+2,ALPS_55,,,,Index_6,GCCAAT,Alps,,Ulm_ALPS_55,patient,,
+2,Reti_MNCplus39_remi,,,,Index_8,ACTTGA,MSC,,,,,
+2,Reti_Fibros,,,,Index_10,TAGCTT,MSC,,,,,
+2,ALPS_548,,,,Index_12,CTTGTA,Alps,,Ulm_ALPS_548,patient,,
+2,R_7_2,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+2,F_10T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+3,Herka_MNC_7,,,,Index_1,ATCACG,MSC,,,,,
+3,ALPS_549,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_549,patient,,
+3,Herka_MSC_7,,,,Index_5,ACAGTG,MSC,,,,,
+3,Herka_MNCplus51_Remi,,,,Index_6,GCCAAT,MSC,,,,,
+3,Herka_Fibros,,,,Index_8,ACTTGA,MSC,,,,,
+3,Dewo_MNC_7,,,,Index_10,TAGCTT,MSC,,,,,
+3,Dewo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,,
+3,R_7_3,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+3,F_11T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+4,Herka_MNC_7,,,,Index_1,ATCACG,MSC,,,,,
+4,ALPS_549,,,,Index_4,TGACCA,Alps,,Ulm_ALPS_549,patient,,
+4,Herka_MSC_7,,,,Index_5,ACAGTG,MSC,,,,,
+4,Herka_MNCplus51_Remi,,,,Index_6,GCCAAT,MSC,,,,,
+4,Herka_Fibros,,,,Index_8,ACTTGA,MSC,,,,,
+4,Dewo_MNC_7,,,,Index_10,TAGCTT,MSC,,,,,
+4,Dewo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,,
+4,R_7_4,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+4,F_12T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+5,Dewo_MNCplus51_Remi,,,,Index_1,ATCACG,MSC,,,,,
+5,Dewo_Fibros,,,,Index_4,TGACCA,MSC,,,,,
+5,P_AML_Bulk_MNC,,,,Index_5,ACAGTG,MSC,,,,,
+5,14_0291,,,,Index_6,GCCAAT,Humangenetik_Wien,,,,,
+5,P_AML_CD34plus_CD41,,,,Index_8,ACTTGA,MSC,,,,,
+5,202_REMI,,,,Index_10,TAGCTT,Inform,,202,,,20202
+5,14_0152,,,,Index_12,CTTGTA,Humangenetik_Wien,,,,,
+5,R_7_5,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+5,F_13T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+6,Dewo_MNCplus51_Remi,,,,Index_1,ATCACG,MSC,,,,,
+6,Dewo_Fibros,,,,Index_4,TGACCA,MSC,,,,,
+6,P_AML_Bulk_MNC,,,,Index_5,ACAGTG,MSC,,,,,
+6,14_0291,,,,Index_6,GCCAAT,Humangenetik_Wien,,,,,
+6,P_AML_CD34plus_CD41,,,,Index_8,ACTTGA,MSC,,,,,
+6,202_REMI,,,,Index_10,TAGCTT,Inform,,202,,,20202
+6,14_0152,,,,Index_12,CTTGTA,Humangenetik_Wien,,,,,
+6,R_7_6,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+6,F_37T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
+7,202_RLPS,,,,Index_1,ATCACG,Inform,,202,,,19635
+7,202_RLPS,,,,Index_4,TGACCA,Humangenetik_Wien,,,,,14_0174
+7,202_RLPS,,,,Index_5,ACAGTG,MSC,,,,,Rova_MNC_7
+7,202_RLPS,,,,Index_6,GCCAAT,MSC,,,,,Rova_MSC_7
+7,202_RLPS,,,,Index_8,ACTTGA,MSC,,,,,Rova_MSCplus41_Remi
+7,202_RLPS,,,,Index_10,TAGCTT,MSC,,,,,Rova_Fibtos
+7,202_RLPS,,,,Index_12,CTTGTA,MSC,,,,,Azem_MNC_7
+7,202_RLPS,,,,Index_7,CAGATC,Amplicon_Rene,,,,,R_7_8
+7,202_RLPS,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,F_44T
+8,202_RLPS,,,,Index_1,ATCACG,Inform,,202,,,19635
+8,14_0174,,,,Index_4,TGACCA,Humangenetik_Wien,,,,,
+8,Rova_MNC_7,,,,Index_5,ACAGTG,MSC,,,,,
+8,Rova_MSC_7,,,,Index_6,GCCAAT,MSC,,,,,
+8,Rova_MSCplus41_Remi,,,,Index_8,ACTTGA,MSC,,,,,
+8,Rova_Fibtos,,,,Index_10,TAGCTT,MSC,,,,,
+8,Azem_MNC_7,,,,Index_12,CTTGTA,MSC,,,,,
+8,R_7_10,,,,Index_7,CAGATC,Amplicon_Rene,,,,,
+8,F_49T,,,,Index_2,CGATGT,Amplicon_Franzi,,,,,
diff --git a/data/samplesheets/141014_SN737_0329_AC4HAUACXX_spike.csv b/data/samplesheets/141014_SN737_0329_AC4HAUACXX_spike.csv
index 169055f7..69d2999a 100644
--- a/data/samplesheets/141014_SN737_0329_AC4HAUACXX_spike.csv
+++ b/data/samplesheets/141014_SN737_0329_AC4HAUACXX_spike.csv
@@ -1,47 +1,47 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,10/14/14,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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,AMH_CD45,,,,Index_12,CTTGTA,Inform_Meisel,,,,
-1,4225_1,,,,Index_4,TGACCA,Inform_Meisel,,,,
-1,4361_1,,,,Index_5,ACAGTG,Inform_Meisel,,,,
-2,Azem_MSC_7,,,,Index_12,CTTGTA,MSC,,,,
-2,Azem_MSCplus29_rem,,,,Index_4,TGACCA,MSC,,,,
-2,Azem_Fibros,,,,Index_5,ACAGTG,MSC,,,,
-3,Lofi_MNC_7,,,,Index_12,CTTGTA,MSC,,,,
-3,Lofi_MSC_7,,,,Index_4,TGACCA,MSC,,,,
-3,Lofi_MNC_plus29_Remi,,,,Index_5,ACAGTG,MSC,,,,
-4,Lofi_Fibros,,,,Index_12,CTTGTA,MSC,,,,
-4,LuHu_MNC_7,,,,Index_4,TGACCA,MSC,,,,
-4,LuHu_MSC_7,,,,Index_5,ACAGTG,MSC,,,,
-5,LuHu_MNC_Remi,,,,Index_12,CTTGTA,MSC,,,,
-5,LuHu_Fibros,,,,Index_4,TGACCA,MSC,,,,
-5,LaBo_MNC_7,,,,Index_5,ACAGTG,MSC,,,,
-6,LaBo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,
-6,LaBo_MNC_Remi,,,,Index_4,TGACCA,MSC,,,,
-6,LaBo_Fibros,,,,Index_5,ACAGTG,MSC,,,,
-7,DaHe_MNC_7,,,,Index_12,CTTGTA,MSC,,,,
-7,DaHe_MSC_7,,,,Index_4,TGACCA,MSC,,,,
-7,DaHe_MNC_plusRemi,,,,Index_5,ACAGTG,MSC,,,,
-8,JoSchplusRez_CD3,,,,Index_12,CTTGTA,Meisel_Ute,,,,
-8,JoSchplusRez_CD10,,,,Index_4,TGACCA,Meisel_Ute,,,,
-8,JoSch_Remi_17705,,,,Index_5,ACAGTG,Meisel_Ute,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,10/14/14,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+1,AMH_CD45,,,,Index_12,CTTGTA,Inform,,,,,
+1,4225_1,,,,Index_4,TGACCA,Inform,,,,,
+1,4361_1,,,,Index_5,ACAGTG,Inform,,,,,
+2,Azem_MSC_7,,,,Index_12,CTTGTA,MSC,,,,,
+2,Azem_MSCplus29_rem,,,,Index_4,TGACCA,MSC,,,,,
+2,Azem_Fibros,,,,Index_5,ACAGTG,MSC,,,,,
+3,Lofi_MNC_7,,,,Index_12,CTTGTA,MSC,,,,,
+3,Lofi_MSC_7,,,,Index_4,TGACCA,MSC,,,,,
+3,Lofi_MNC_plus29_Remi,,,,Index_5,ACAGTG,MSC,,,,,
+4,Lofi_Fibros,,,,Index_12,CTTGTA,MSC,,,,,
+4,LuHu_MNC_7,,,,Index_4,TGACCA,MSC,,,,,
+4,LuHu_MSC_7,,,,Index_5,ACAGTG,MSC,,,,,
+5,LuHu_MNC_Remi,,,,Index_12,CTTGTA,MSC,,,,,
+5,LuHu_Fibros,,,,Index_4,TGACCA,MSC,,,,,
+5,LaBo_MNC_7,,,,Index_5,ACAGTG,MSC,,,,,
+6,LaBo_MSC_7,,,,Index_12,CTTGTA,MSC,,,,,
+6,LaBo_MNC_Remi,,,,Index_4,TGACCA,MSC,,,,,
+6,LaBo_Fibros,,,,Index_5,ACAGTG,MSC,,,,,
+7,DaHe_MNC_7,,,,Index_12,CTTGTA,MSC,,,,,
+7,DaHe_MSC_7,,,,Index_4,TGACCA,MSC,,,,,
+7,DaHe_MNC_plusRemi,,,,Index_5,ACAGTG,MSC,,,,,
+8,705_TRREMI,,,,Index_12,CTTGTA,Inform,,705,,,JoSchplusRez_CD3
+8,JoSchplusRez_CD10,,,,Index_4,TGACCA,Meisel_Ute,,,,,
+8,705_REMI,,,,Index_5,ACAGTG,Inform,,705,,,JoSch_Remi_17705
diff --git a/data/samplesheets/150421_SN737_0355_BC65R3ACXX_spike.csv b/data/samplesheets/150421_SN737_0355_BC65R3ACXX_spike.csv
index cca77ed0..0fc8d80a 100644
--- a/data/samplesheets/150421_SN737_0355_BC65R3ACXX_spike.csv
+++ b/data/samplesheets/150421_SN737_0355_BC65R3ACXX_spike.csv
@@ -1,81 +1,81 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,04/21/15,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-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
-1,05_2837_BM,,,,Index_1,ATCACG,Donor_Dervied_Leukemia_Fischer,,,,
-1,12_4018_PB,,,,Index_4,TGACCA,Donor_Dervied_Leukemia_Fischer,,,,
-1,14_7557_PB,,,,Index_5,ACAGTG,Donor_Dervied_Leukemia_Fischer,,,,
-1,14_7564_BM,,,,Index_6,GCCAAT,Donor_Dervied_Leukemia_Fischer,,,,
-1,2005,,,,Index_8,ACTTGA,Donor_Dervied_Leukemia_Fischer,,,,
-1,UKDID_21P,,,,Index_10,TAGCTT,UKDID,,UKDID_21,patient,
-1,UKDID_21F1_M,,,,Index_12,CTTGTA,UKDID,,UKDID_21,,
-1,82C,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-2,05_2837_BM,,,,Index_1,ATCACG,Donor_Dervied_Leukemia_Fischer,,,,
-2,12_4018_PB,,,,Index_4,TGACCA,Donor_Dervied_Leukemia_Fischer,,,,
-2,14_7557_PB,,,,Index_5,ACAGTG,Donor_Dervied_Leukemia_Fischer,,,,
-2,14_7564_BM,,,,Index_6,GCCAAT,Donor_Dervied_Leukemia_Fischer,,,,
-2,2005,,,,Index_8,ACTTGA,Donor_Dervied_Leukemia_Fischer,,,,
-2,UKDID_21P,,,,Index_10,TAGCTT,UKDID,,UKDID_21,patient,
-2,UKDID_21F1_M,,,,Index_12,CTTGTA,UKDID,,UKDID_21,,
-2,82PB,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-3,UKDID_21F2_V,,,,Index_1,ATCACG,UKDID,,UKDID_21,,
-3,UKDID_21B_Br,,,,Index_4,TGACCA,UKDID,,UKDID_21,,
-3,xxx_M,,,,Index_5,ACAGTG,UKDID,,,,
-3,15D2926,,,,Index_6,GCCAAT,Rotterdam_Borkhardt,,,,
-3,15D2930,,,,Index_8,ACTTGA,Rotterdam_Borkhardt,,,,
-3,15D2792,,,,Index_10,TAGCTT,Rotterdam_Borkhardt,,,,
-3,15D2869,,,,Index_12,CTTGTA,Rotterdam_Borkhardt,,,,
-3,11T,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-4,UKDID_21F2_V,,,,Index_1,ATCACG,UKDID,,UKDID_21,,
-4,UKDID_21B_Br,,,,Index_4,TGACCA,UKDID,,UKDID_21,,
-4,xxx_M,,,,Index_5,ACAGTG,UKDID,,,,
-4,15D2926,,,,Index_6,GCCAAT,Rotterdam_Borkhardt,,,,
-4,15D2930,,,,Index_8,ACTTGA,Rotterdam_Borkhardt,,,,
-4,15D2792,,,,Index_10,TAGCTT,Rotterdam_Borkhardt,,,,
-4,68C,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-4,15D2869,,,,Index_12,CTTGTA,Rotterdam_Borkhardt,,,,
-5,77,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-5,21573,,,,Index_1,ATCACG,Inform_Meisel,,,,
-5,21619,,,,Index_4,TGACCA,Inform_Meisel,,,,
-5,21617,,,,Index_5,ACAGTG,Inform_Meisel,,,,
-5,21606,,,,Index_6,GCCAAT,Inform_Meisel,,,,
-5,20653,,,,Index_8,ACTTGA,Inform_Meisel,,,,
-5,3963,,,,Index_10,TAGCTT,ALL_Hauer,,,,
-5,41082,,,,Index_12,CTTGTA,ALL_Hauer,,,,
-6,21573,,,,Index_1,ATCACG,Inform_Meisel,,,,
-6,21619,,,,Index_4,TGACCA,Inform_Meisel,,,,
-6,21617,,,,Index_5,ACAGTG,Inform_Meisel,,,,
-6,21606,,,,Index_6,GCCAAT,Inform_Meisel,,,,
-6,20653,,,,Index_8,ACTTGA,Inform_Meisel,,,,
-6,3963,,,,Index_10,TAGCTT,ALL_Hauer,,,,
-6,41082,,,,Index_12,CTTGTA,ALL_Hauer,,,,
-6,82_HSC,,,,Index_2,CGATGT,Amplicon_Maus,,,,
-7,2771_DX,,,,Index_1,ATCACG,dsALL,,2771,tumor,
-7,2771_Rem,,,,Index_4,TGACCA,dsALL,,2771,healthy,
-7,2771_Rel_I,,,,Index_5,ACAGTG,dsALL,,2771,tumor,
-7,2771_Rel_II,,,,Index_6,GCCAAT,dsALL,,2771,tumor,
-7,41852,,,,Index_8,ACTTGA,ALL_Hauer,,,,
-8,2771_DX,,,,Index_1,ATCACG,dsALL,,2771,tumor,
-8,2771_Rem,,,,Index_4,TGACCA,dsALL,,2771,healthy,
-8,2771_Rel_I,,,,Index_5,ACAGTG,dsALL,,2771,tumor,
-8,2771_Rel_II,,,,Index_6,GCCAAT,dsALL,,2771,tumor,
-8,41852,,,,Index_8,ACTTGA,ALL_Hauer,,,,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,04/21/15,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Katayoun Alemazkour/Michael Gombert,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+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,spike_original_but_wrong_sample_id
+1,05_2837_BM,,,,Index_1,ATCACG,Donor_Dervied_Leukemia_Fischer,,,,,
+1,12_4018_PB,,,,Index_4,TGACCA,Donor_Dervied_Leukemia_Fischer,,,,,
+1,14_7557_PB,,,,Index_5,ACAGTG,Donor_Dervied_Leukemia_Fischer,,,,,
+1,14_7564_BM,,,,Index_6,GCCAAT,Donor_Dervied_Leukemia_Fischer,,,,,
+1,2005,,,,Index_8,ACTTGA,Donor_Dervied_Leukemia_Fischer,,,,,
+1,UKDID_21P,,,,Index_10,TAGCTT,UKDID,,UKDID_21,patient,,
+1,UKDID_21F1_M,,,,Index_12,CTTGTA,UKDID,,UKDID_21,,,
+1,82C,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+2,05_2837_BM,,,,Index_1,ATCACG,Donor_Dervied_Leukemia_Fischer,,,,,
+2,12_4018_PB,,,,Index_4,TGACCA,Donor_Dervied_Leukemia_Fischer,,,,,
+2,14_7557_PB,,,,Index_5,ACAGTG,Donor_Dervied_Leukemia_Fischer,,,,,
+2,14_7564_BM,,,,Index_6,GCCAAT,Donor_Dervied_Leukemia_Fischer,,,,,
+2,2005,,,,Index_8,ACTTGA,Donor_Dervied_Leukemia_Fischer,,,,,
+2,UKDID_21P,,,,Index_10,TAGCTT,UKDID,,UKDID_21,patient,,
+2,UKDID_21F1_M,,,,Index_12,CTTGTA,UKDID,,UKDID_21,,,
+2,82PB,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+3,UKDID_21F2_V,,,,Index_1,ATCACG,UKDID,,UKDID_21,,,
+3,UKDID_21B_Br,,,,Index_4,TGACCA,UKDID,,UKDID_21,,,
+3,xxx_M,,,,Index_5,ACAGTG,UKDID,,,,,
+3,15D2926,,,,Index_6,GCCAAT,Rotterdam_Borkhardt,,,,,
+3,15D2930,,,,Index_8,ACTTGA,Rotterdam_Borkhardt,,,,,
+3,15D2792,,,,Index_10,TAGCTT,Rotterdam_Borkhardt,,,,,
+3,15D2869,,,,Index_12,CTTGTA,Rotterdam_Borkhardt,,,,,
+3,11T,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+4,UKDID_21F2_V,,,,Index_1,ATCACG,UKDID,,UKDID_21,,,
+4,UKDID_21B_Br,,,,Index_4,TGACCA,UKDID,,UKDID_21,,,
+4,xxx_M,,,,Index_5,ACAGTG,UKDID,,,,,
+4,15D2926,,,,Index_6,GCCAAT,Rotterdam_Borkhardt,,,,,
+4,15D2930,,,,Index_8,ACTTGA,Rotterdam_Borkhardt,,,,,
+4,15D2792,,,,Index_10,TAGCTT,Rotterdam_Borkhardt,,,,,
+4,68C,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+4,15D2869,,,,Index_12,CTTGTA,Rotterdam_Borkhardt,,,,,
+5,77,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+5,107_TRLPS,,,,Index_1,ATCACG,Inform,,107,,,21573
+5,107_TREMI,,,,Index_4,TGACCA,Inform,,107,,,21619
+5,21617,,,,Index_5,ACAGTG,Inform,,,,,
+5,107_REMI,,,,Index_6,GCCAAT,Inform,,107,,,21606
+5,107_INIT,,,,Index_8,ACTTGA,Inform,,107,,,20653
+5,3963,,,,Index_10,TAGCTT,Inform,,,,,
+5,41082,,,,Index_12,CTTGTA,Inform,,,,,
+6,107_TRLPS,,,,Index_1,ATCACG,Inform,,107,,,21573
+6,107_TREMI,,,,Index_4,TGACCA,Inform,,107,,,21619
+6,21617,,,,Index_5,ACAGTG,Inform,,,,,
+6,107_REMI,,,,Index_6,GCCAAT,Inform,,107,,,21606
+6,107_INIT,,,,Index_8,ACTTGA,Inform,,107,,,20653
+6,3963,,,,Index_10,TAGCTT,ALL_Hauer,,,,,
+6,41082,,,,Index_12,CTTGTA,ALL_Hauer,,,,,
+6,82_HSC,,,,Index_2,CGATGT,Amplicon_Maus,,,,,
+7,2771_DX,,,,Index_1,ATCACG,dsALL,,2771,tumor,,
+7,2771_Rem,,,,Index_4,TGACCA,dsALL,,2771,healthy,,
+7,2771_Rel_I,,,,Index_5,ACAGTG,dsALL,,2771,tumor,,
+7,2771_Rel_II,,,,Index_6,GCCAAT,dsALL,,2771,tumor,,
+7,41852,,,,Index_8,ACTTGA,ALL_Hauer,,,,,
+8,2771_DX,,,,Index_1,ATCACG,dsALL,,2771,tumor,,
+8,2771_Rem,,,,Index_4,TGACCA,dsALL,,2771,healthy,,
+8,2771_Rel_I,,,,Index_5,ACAGTG,dsALL,,2771,tumor,,
+8,2771_Rel_II,,,,Index_6,GCCAAT,dsALL,,2771,tumor,,
+8,41852,,,,Index_8,ACTTGA,ALL_Hauer,,,,,
diff --git a/data/samplesheets/150522_SN737_0356_AC65R2ACXX_spike.csv b/data/samplesheets/150522_SN737_0356_AC65R2ACXX_spike.csv
index 0d432547..aadce0f1 100644
--- a/data/samplesheets/150522_SN737_0356_AC65R2ACXX_spike.csv
+++ b/data/samplesheets/150522_SN737_0356_AC65R2ACXX_spike.csv
@@ -1,72 +1,72 @@
-[Header],,,,,,,,,,,
-IEMFileVersion,5,,,,,,,,,,
-Date,05/22/15,,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,,
-Application,HiSeq FASTQ Only,,,,,,,,,,
-Instrument Type,HiSeq 1500/2500,,,,,,,,,,
-Assay,Agilent_Sure_SelectXT,,,,,,,,,,
-Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,
-Chemistry,Default,,,,,,,,,,
-Description,,,,,,,,,,,
-Operator,Michael Gombert/Katayoun Alemazkour,,,,,,,,,,
-Investigator,Ute Fischer/Roland Meisel/Julia Hauer,,,,,,,,,,
-Backup_NAS_name,Phex,,,,,,,,,,
-kind_of_run,2x100bp,,,,,,,,,,
-[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
-1,21316,,,,A01,ATGCCTAA,Inform_Meisel,,,,
-1,21318,,,,B01,GAATCTGA,Inform_Meisel,,,,
-1,20861,,,,C01,AACGTGAT,Inform_Meisel,,,,
-1,19221,,,,D01,CACTTCGA,Inform_Meisel,,,,
-1,20246,,,,E01,GCCAAGAC,Inform_Meisel,,,,
-1,20802,,,,F01,GACTAGTA,Inform_Meisel,,,,
-1,21315,,,,G01,ATTGGCTC,Inform_Meisel,,,,
-2,21316,,,,A01,ATGCCTAA,Inform_Meisel,,,,
-2,21318,,,,B01,GAATCTGA,Inform_Meisel,,,,
-2,20861,,,,C01,AACGTGAT,Inform_Meisel,,,,
-2,19221,,,,D01,CACTTCGA,Inform_Meisel,,,,
-2,20246,,,,E01,GCCAAGAC,Inform_Meisel,,,,
-2,20802,,,,F01,GACTAGTA,Inform_Meisel,,,,
-2,21315,,,,G01,ATTGGCTC,Inform_Meisel,,,,
-3,21317,,,,A01,ATGCCTAA,Inform_Meisel,,,,
-3,19925,,,,B01,GAATCTGA,Inform_Meisel,,,,
-3,18824,,,,C01,AACGTGAT,Inform_Meisel,,,,
-3,19814,,,,D01,CACTTCGA,Inform_Meisel,,,,
-3,21098,,,,E01,GCCAAGAC,Inform_Meisel,,,,
-3,21162,,,,F01,GACTAGTA,Inform_Meisel,,,,
-3,17225,,,,G01,ATTGGCTC,Inform_Meisel,,,,
-4,21317,,,,A01,ATGCCTAA,Inform_Meisel,,,,
-4,19925,,,,B01,GAATCTGA,Inform_Meisel,,,,
-4,18824,,,,C01,AACGTGAT,Inform_Meisel,,,,
-4,19814,,,,D01,CACTTCGA,Inform_Meisel,,,,
-4,21098,,,,E01,GCCAAGAC,Inform_Meisel,,,,
-4,21162,,,,F01,GACTAGTA,Inform_Meisel,,,,
-4,17225,,,,G01,ATTGGCTC,Inform_Meisel,,,,
-5,ALPS_25a,,,,A01,ATGCCTAA,Alps,,ALPS_25,father,
-5,ALPS_25b,,,,B01,GAATCTGA,Alps,,ALPS_25,mother,
-5,ALPS_11c,,,,C01,AACGTGAT,Alps,,ALPS_11,sibling,
-5,ALPS_18a,,,,D01,CACTTCGA,Alps,,ALPS_18,father,
-5,ALPS_18b,,,,E01,GCCAAGAC,Alps,,ALPS_18,mother,
-5,ALPS_26a,,,,F01,GACTAGTA,Alps,,ALPS_26,father,
-5,ALPS_26b,,,,G01,ATTGGCTC,Alps,,ALPS_26,mother,
-6,ALPS_25a,,,,A01,ATGCCTAA,Alps,,ALPS_25,father,
-6,ALPS_25b,,,,B01,GAATCTGA,Alps,,ALPS_25,mother,
-6,ALPS_11c,,,,C01,AACGTGAT,Alps,,ALPS_11,sibling,
-6,ALPS_18a,,,,D01,CACTTCGA,Alps,,ALPS_18,father,
-6,ALPS_18b,,,,E01,GCCAAGAC,Alps,,ALPS_18,mother,
-6,ALPS_26a,,,,F01,GACTAGTA,Alps,,ALPS_26,father,
-6,ALPS_26b,,,,G01,ATTGGCTC,Alps,,ALPS_26,mother,
-7,ALPS_25,,,,A01,ATGCCTAA,Alps,,ALPS_25,patient,
-7,ALPS_26,,,,B01,GAATCTGA,Alps,,ALPS_26,patient,
-8,ALPS_25,,,,A01,ATGCCTAA,Alps,,ALPS_25,patient,
-8,ALPS_26,,,,B01,GAATCTGA,Alps,,ALPS_26,patient,
-7,33C,,,,Index_19,GTGAAA,Maus_Hauer,,33,healthy,
-8,58C,,,,Index_19,GTGAAA,Maus_Hauer,,58,healthy,
+[Header],,,,,,,,,,,,
+IEMFileVersion,5,,,,,,,,,,,
+Date,05/22/15,,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,,
+Application,HiSeq FASTQ Only,,,,,,,,,,,
+Instrument Type,HiSeq 1500/2500,,,,,,,,,,,
+Assay,Agilent_Sure_SelectXT,,,,,,,,,,,
+Index Adapters,Agilent_Sure_SelectXT,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,,
+Description,,,,,,,,,,,,
+Operator,Michael Gombert/Katayoun Alemazkour,,,,,,,,,,,
+Investigator,Ute Fischer/Roland Meisel/Julia Hauer,,,,,,,,,,,
+Backup_NAS_name,Phex,,,,,,,,,,,
+kind_of_run,2x100bp,,,,,,,,,,,
+[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,spike_original_but_wrong_sample_id
+1,316_REMI,,,,A01,ATGCCTAA,Inform,,316,,,21316
+1,318_REMI,,,,B01,GAATCTGA,Inform,,318,,,21318
+1,316_TREMI,,,,C01,AACGTGAT,Inform,,316,,,20861
+1,318_TREMI,,,,D01,CACTTCGA,Inform,,318,,,19221
+1,705_TREMI,,,,E01,GCCAAGAC,Inform,,705,,,20246
+1,202_TREMI,,,,F01,GACTAGTA,Inform,,202,,,20802
+1,316_INIT,,,,G01,ATTGGCTC,Inform,,316,,,21315
+2,316_REMI,,,,A01,ATGCCTAA,Inform,,316,,,21316
+2,318_REMI,,,,B01,GAATCTGA,Inform,,318,,,21318
+2,316_TREMI,,,,C01,AACGTGAT,Inform,,316,,,20861
+2,318_TREMI,,,,D01,CACTTCGA,Inform,,318,,,19221
+2,705_TREMI,,,,E01,GCCAAGAC,Inform,,705,,,20246
+2,202_TREMI,,,,F01,GACTAGTA,Inform,,202,,,20802
+2,316_INIT,,,,G01,ATTGGCTC,Inform,,316,,,21315
+3,318_INIT,,,,A01,ATGCCTAA,Inform,,318,,,21317
+3,316_RLPS,,,,B01,GAATCTGA,Inform,,316,,,19925
+3,318_RLPS,,,,C01,AACGTGAT,Inform,,318,,,18824
+3,705_RRLPS,,,,D01,CACTTCGA,Inform,,705,,,19814
+3,316_TRLPS,,,,E01,GCCAAGAC,Inform,,316,,,21098
+3,318_TRLPS,,,,F01,GACTAGTA,Inform,,318,,,21162
+3,705_RLPS,,,,G01,ATTGGCTC,Inform,,705,,,17225
+4,318_INIT,,,,A01,ATGCCTAA,Inform,,318,,,21317
+4,316_RLPS,,,,B01,GAATCTGA,Inform,,316,,,19925
+4,318_RLPS,,,,C01,AACGTGAT,Inform,,318,,,18824
+4,705_RRLPS,,,,D01,CACTTCGA,Inform,,705,,,19814
+4,316_TRLPS,,,,E01,GCCAAGAC,Inform,,316,,,21098
+4,318_TRLPS,,,,F01,GACTAGTA,Inform,,318,,,21162
+4,705_RLPS,,,,G01,ATTGGCTC,Inform,,705,,,17225
+5,ALPS_25a,,,,A01,ATGCCTAA,Alps,,ALPS_25,father,,
+5,ALPS_25b,,,,B01,GAATCTGA,Alps,,ALPS_25,mother,,
+5,ALPS_11c,,,,C01,AACGTGAT,Alps,,ALPS_11,sibling,,
+5,ALPS_18a,,,,D01,CACTTCGA,Alps,,ALPS_18,father,,
+5,ALPS_18b,,,,E01,GCCAAGAC,Alps,,ALPS_18,mother,,
+5,ALPS_26a,,,,F01,GACTAGTA,Alps,,ALPS_26,father,,
+5,ALPS_26b,,,,G01,ATTGGCTC,Alps,,ALPS_26,mother,,
+6,ALPS_25a,,,,A01,ATGCCTAA,Alps,,ALPS_25,father,,
+6,ALPS_25b,,,,B01,GAATCTGA,Alps,,ALPS_25,mother,,
+6,ALPS_11c,,,,C01,AACGTGAT,Alps,,ALPS_11,sibling,,
+6,ALPS_18a,,,,D01,CACTTCGA,Alps,,ALPS_18,father,,
+6,ALPS_18b,,,,E01,GCCAAGAC,Alps,,ALPS_18,mother,,
+6,ALPS_26a,,,,F01,GACTAGTA,Alps,,ALPS_26,father,,
+6,ALPS_26b,,,,G01,ATTGGCTC,Alps,,ALPS_26,mother,,
+7,ALPS_25,,,,A01,ATGCCTAA,Alps,,ALPS_25,patient,,
+7,ALPS_26,,,,B01,GAATCTGA,Alps,,ALPS_26,patient,,
+8,ALPS_25,,,,A01,ATGCCTAA,Alps,,ALPS_25,patient,,
+8,ALPS_26,,,,B01,GAATCTGA,Alps,,ALPS_26,patient,,
+7,33C,,,,Index_19,GTGAAA,Maus_Hauer,,33,healthy,,
+8,58C,,,,Index_19,GTGAAA,Maus_Hauer,,58,healthy,,
diff --git a/data/samplesheets/160922_SN737_0395_BC92B7ACXX_spike.csv b/data/samplesheets/160922_SN737_0395_BC92B7ACXX_spike.csv
index 37043a18..884290d6 100644
--- a/data/samplesheets/160922_SN737_0395_BC92B7ACXX_spike.csv
+++ b/data/samplesheets/160922_SN737_0395_BC92B7ACXX_spike.csv
@@ -24,31 +24,31 @@ 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
-1,705_TRANS,,,,A01,ATGCCTAA,INFORM,,,,
-1,705_TTRANS,,,,B01,GAATCTGA,INFORM,,,,
-1,705_TTRLPS,,,,C01,AACGTGAT,INFORM,,,,
-1,FIS_TRLPS_b,,,,F01,GACTAGTA,INFORM,,,,
-1,FIS_TTRANS,,,,G01,ATTGGCTC,INFORM,,,,
-1,FIS_TTRLPS,,,,H01,GATGAATC,INFORM,,,,
-2,705_TRANS,,,,A01,ATGCCTAA,INFORM,,,,
-2,705_TTRANS,,,,B01,GAATCTGA,INFORM,,,,
-2,705_TTRLPS,,,,C01,AACGTGAT,INFORM,,,,
-2,FIS_TRLPS_b,,,,F01,GACTAGTA,INFORM,,,,
-2,FIS_TTRANS,,,,G01,ATTGGCTC,INFORM,,,,
-2,FIS_TTRLPS,,,,H01,GATGAATC,INFORM,,,,
+1,705_TRANS,,,,A01,ATGCCTAA,Inform,,705,,
+1,705_TTRANS,,,,B01,GAATCTGA,Inform,,705,,
+1,705_TTRLPS,,,,C01,AACGTGAT,Inform,,705,,
+1,FIS_TRLPS_b,,,,F01,GACTAGTA,Inform,,FIS,,
+1,FIS_TTRANS,,,,G01,ATTGGCTC,Inform,,FIS,,
+1,FIS_TTRLPS,,,,H01,GATGAATC,Inform,,FIS,,
+2,705_TRANS,,,,A01,ATGCCTAA,Inform,,705,,
+2,705_TTRANS,,,,B01,GAATCTGA,Inform,,705,,
+2,705_TTRLPS,,,,C01,AACGTGAT,Inform,,705,,
+2,FIS_TRLPS_b,,,,F01,GACTAGTA,Inform,,FIS,,
+2,FIS_TTRANS,,,,G01,ATTGGCTC,Inform,,FIS,,
+2,FIS_TTRLPS,,,,H01,GATGAATC,Inform,,FIS,,
 3,ALPS_46p1,,,,A01,ATGCCTAA,Alps,,ALPS_46,patient,
 3,ALPS_46p2,,,,B01,GAATCTGA,Alps,also sick,ALPS_46,sibling,
 3,ALPS_46_a,,,,C01,AACGTGAT,Alps,,ALPS_46,father,
 3,ALPS_46_b,,,,D01,CACTTCGA,Alps,,ALPS_46,mother,
 3,ALPS_47e,,,,E01,GCCAAGAC,Alps,,ALPS_47,sibling,
-3,202_TTREMI,,,,G01,ATTGGCTC,INFORM,,,,
+3,202_TTREMI,,,,G01,ATTGGCTC,Inform,,202,,
 3,anonymous_person,,,,H01,GATGAATC,MSC,,anonymous_person,,
 4,ALPS_46p1,,,,A01,ATGCCTAA,Alps,,ALPS_46,patient,
 4,ALPS_46p2,,,,B01,GAATCTGA,Alps,also sick,ALPS_46,sibling,
 4,ALPS_46_a,,,,C01,AACGTGAT,Alps,,ALPS_46,father,
 4,ALPS_46_b,,,,D01,CACTTCGA,Alps,,ALPS_46,mother,
 4,ALPS_47e,,,,E01,GCCAAGAC,Alps,,ALPS_47,sibling,
-4,202_TTREMI,,,,G01,ATTGGCTC,INFORM,,,,
+4,202_TTREMI,,,,G01,ATTGGCTC,Inform,,202,,
 4,anonymous_person,,,,H01,GATGAATC,MSC,,anonymous_person,,
 5,KB0099_c,,,,F01,GACTAGTA,Keimbahn,,KB0099,patient,
 5,KB0058_m,,,,C01,AACGTGAT,Keimbahn,,KB0058,mother,
diff --git a/data/samplesheets/171116_SN737_0427_BCAMDYACXX_spike.csv b/data/samplesheets/171116_SN737_0427_BCAMDYACXX_spike.csv
index cc174ec7..4b36f854 100644
--- a/data/samplesheets/171116_SN737_0427_BCAMDYACXX_spike.csv
+++ b/data/samplesheets/171116_SN737_0427_BCAMDYACXX_spike.csv
@@ -55,12 +55,12 @@ Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Pro
 6,KB0120_m,,,,B01,GAATCTGA,Keimbahn,Set3,KB0120,mother,
 6,KB0149_c,,,,C01,AACGTGAT,Keimbahn,Set3,KB0149,patient,
 6,KB0149_f,,,,D01,CACTTCGA,Keimbahn,Set3,KB0149,father,
-7,215_TTRLPS,,,,A01,ATGCCTAA,INFORM,Set 4,,,
+7,215_TTRLPS,,,,A01,ATGCCTAA,Inform,Set 4,215,,
 7,ALPS_57,,,,F01,GACTAGTA,Alps,Set 4,ALPS_57,patient,
 7,ALPS_57a,,,,G01,ATTGGCTC,Alps,Set 4,ALPS_57,father,
 7,ALPS_57b,,,,H01,GATGAATC,Alps,,ALPS_57,mother,
 7,KB0149_m,,,,E01,GCCAAGAC,Keimbahn,,KB0149,mother,
-8,215_TTRLPS,,,,A01,ATGCCTAA,INFORM,,,,
+8,215_TTRLPS,,,,A01,ATGCCTAA,Inform,,215,,
 8,ALPS_57,,,,F01,GACTAGTA,Alps,Set 4,ALPS_57,patient,
 8,ALPS_57a,,,,G01,ATTGGCTC,Alps,Set 4,ALPS_57,father,
 8,ALPS_57b,,,,H01,GATGAATC,Alps,,ALPS_57,mother,