Can't load primary/alignment files only

[ces]

If we just want to load primary files e.g. cram, crai, flagstat and not qc files - as after ad-hoc reprocessing - the npg_publish_illumina_run.pl script currently fails as it relies on the bam_flagstats.json file to find the read count for the cram meta data.

e.g. npg_publish_illumina_run.pl --driver-type samplesheet --id_run=$run --include=lane$lane --exclude=lane$lane/qc --verbose --source-directory=.

2019/01/28 16:59:01 ERROR WTSI.NPG.HTS.Illumina.RunPublisher - Unexpected error in publish_files: Found 0 matching '(?^msx:/6683_4#13.bam_flagstats.json$)' where one was expected: [] at /blah/lib/perl5/WTSI/NPG/HTS/Illumina/RunPublisher.pm line 696.

Be good to have a option or way to exclude qc files from loading as previously.

[kjsanger]

Yes, this is a result of the exclusion pattern excluding a file that is required to load one of the included files. To do this we'd have to add the concept of a filtered resultset (containing just the files you want to load) which is a subset of the full resultset (which contains other files, you don't want to load, but may want to operate on).