feature request: detect when a run needs to be demultiplexed as single lane

[georgemarselis-nvi]

there is at least one run that needs to be demultiplexed as a single lane

alter the bcl2fast() method to catch a failure, check if bcl2fastq has complained appropriately and restart mutliplexing with appropriate command line.

Things that need to be figured out:

What was the relevant RunID:
What was the altered command line:
What was the difference with regular command line:

from a quick investigation:

find . -iname 02_demultiplex.log -exec grep -i '0 error' {} ;

find . -iname 02_demultiplex.log -exec grep -inl '1 warn' {} ; | sed 's/// /g' | awk '{ print $2 }'

210115_M06578_0042_000000000-JF7MT_demultiplex
210304_M06578_0044_000000000-JF7WC_demultiplex
210311_M06578_0045_000000000-JF7N3_demultiplex
210317_M06578_0046_000000000-DB8C6_demultiplex
210319_M06578_0047_000000000-JF8D2_demultiplex
210325_M06578_0048_000000000-JF8G4_demultiplex
210415_M06578_0049_000000000-JL3JW_demultiplex
210422_M06578_0050_000000000-JKHD4_demultiplex
210512_M06578_0051_000000000-JL3FM_demultiplex
210521_M06578_0052_000000000-JKW2V_demultiplex
210603_M06578_0053_000000000-JKHBM_demultiplex
210610_M06578_0054_000000000-DC5G2_demultiplex
210611_M06578_0055_000000000-JN9DH_demultiplex
210618_M06578_0056_000000000-JN84N_demultiplex
210623_M06578_0057_000000000-DC4KC_demultiplex
210625_M06578_0058_000000000-JMJN4_demultiplex
210806_M06578_0059_000000000-JN8RR_demultiplex
210813_M06578_0060_000000000-JN8MH_demultiplex
210818_M06578_0061_000000000-DC5DP_demultiplex
210827_M06578_0062_000000000-JR8RK_demultiplex
201218_M06578_0041_000000000-JF7TM_demultiplex
210212_M06578_0043_000000000-DB8DF_demultiplex
210830_M06578_0063_000000000-JRC67_demultiplex
210902_M06578_0064_000000000-DC5Y9_demultiplex
211001_M06578_0067_000000000-JV8DG_demultiplex
211015_M06578_0069_000000000-JVY98_demultiplex
211022_NB552450_0003_AH725HAFX3_demultiplex
220221_M06578_0090_000000000-DFMWT_demultiplex
220422_M06578_0098_000000000-K887T_demultiplex
221103_NB552450_0010_AHJGKKBGXL_demultiplex
220314_M06578_0091_000000000-DFM6K_demultiplex.orig

problem is that the issue came up only once in the old host.

I will look for the same in my workstation copy of the data. If i don't find anything i'll just re-demultiplex everything over a weekend.