grouped_gtc_to_bed fails when one of the GTC files are corrupted

[shukwong]

It seems that when the pipeline is run with only GTC files as input, and that one of the GTC files is corrupted, the grouped_gtc_to_bed task that the cluster_group the GTC file is in will fail without much information given.
It would be good that:

• Option 1: report which GTC file is corrupted and fail gracefully
• Option 2: report which GTC file is corrupted and continue.

[rajwanir]

I think I slightly misunderstood the issue. It's refering to "corrupted" such that the file exists but is not usable and with GTC entry point.

While writing IDAT->GTC->BCF->Plink/BED workflow, I encountered some samples would fail the conversion IDAT>GTC due to IDAT being corrupted i.e. file exists but not usable. I took the option 2 route in that case as described in issue #370 and fixed with 77b172c in PR #359 (yet to be merged into default). With this fix, any samples that have a corrupt IDAT (exists but fails GTC creation), it will flag them as is_missing_gtc=True in samplesheet, skip them from further analysis and continue.

This would be only applicable if user starts with IDATs. If GTC is entry point is used, similar check and skip function need to be implemented. Currently, not addressed. Sorry.

[shukwong]

No worries. Thanks for looking into this, Rahim!