calling `interop_summary` and `interop_index-summary` when using bcl-convert

[BCArg]

I am switching from bcl2fastq to bcl-convert. In order to get and store run metrics I run interop_summary and interop_index-summary (both installed with conda) in the run directory where the following is present:

1. RunInfo.xml
2. a folder named InterOp - generated by bcl2fastq

bcl-convert does not generate the InterOp folder, as far as I can tell, and according to this documentation, this is not possible.

Is it possible to use interop_summary and interop_index-summary on the files generated by bcl-convert? If not, is there an equivalent program that can be used?

[ezralanglois]

You could write a script that copies IndexMetricsOut.bin from the bclconvert directory to either the run's InterOp directory or some new run folder's InterOp directory.

If you go with the second one, then you should copy InterOp/TileMetricsOut.bin and RunInfo.xml

[BCArg]

IndexMetricsOut.bin and RunInfo.xml are fine, they are generated by bcl-convert. The content of the Reports folder is shown below:

-rw-rw-r-- 1 ngs ngs   14312  9. Nov 12:21 Adapter_Metrics.csv
-rw-rw-r-- 1 ngs ngs   15882  9. Nov 12:21 Demultiplex_Stats.csv
-rw-rw-r-- 1 ngs ngs   49110  9. Nov 12:00 fastq_list.csv
-rw-rw-r-- 1 ngs ngs      35  9. Nov 12:21 Index_Hopping_Counts.csv
-rw-rw-r-- 1 ngs ngs 7883617  9. Nov 12:21 IndexMetricsOut.bin
-rw-rw-r-- 1 ngs ngs   16423  9. Nov 12:00 RunInfo.xml
-rw-rw-r-- 1 ngs ngs    6330  9. Nov 12:00 SampleSheet.csv
-rw-rw-r-- 1 ngs ngs    5422  9. Nov 12:21 Top_Unknown_Barcodes.csv

It appears that TileMetricsOut.bin is also required, is it possible to generate this file with bcl-convert?

[ezralanglois]

Yes, TileMetricsOut.bin is required. It is in the run folder and is not produced by bcl-convert