Possibility have multiple Ilmn index types in one samplesheet

[remiolsen]

Currently this functionality exist in a way. The program will correctly run demultiplexing twice,
however it doesn't do it correctly - all the samples get zero reads.
There's also a need to sort out how the file handling is to be done in this situation

Example anglerfish samplesheet:

P9712_130,truseq_dual,GAGATTCC,TAATCTTA
P12754_101_1,truseq,GAAACCCT

Excerpt of anglerfish_stats.txt

truseq_dual_len8:
105608	input reads
38876	reads aligning to adaptor sequences (36.81%)
0	aligned reads matching both I7 and I5 adaptor (0.00%)
38499	aligned reads matching only I7 or I5 adaptor (99.03%)
0	aligned reads matching multiple I7/I5 adaptor pairs (0.00%)
377	aligned reads with uncategorized alignments (0.97%)
sample_name	#reads
P9712_130	0
....
P12754_101_1	0

The way I have solved this problem before is to split these types of setups in to two samplesheets and run them separately.