Related Issues (20)
- `annotate` can fail with 'Failed to instantiate plugin GADO' HOT 1
- Succesfull pipeline execution if `individual_id` doesn't exist in vcf
- VCF index not created with HTSlib doesn't work
- Report can contain data of samples not in sample sheet
- Support .sam input in addition to .bam and .cram
- cuteSV can fail based on `~` content on host machine
- Report crashed in detail view for long read data (reads to big for genome browser) HOT 1
- `nf-cram_str_straglr_call` can produce unsorted `vcf`
- Error merging SVs: The REF prefixes differ: A vs N (1,1) HOT 1
- filter samples somehow removes some INFO headers
- VIP errors if 2 filenames in the input are identical
- Add AlphaMissense to annotations HOT 1
- ncER GRCh38 data contains overlapping values
- Non-deterministic consequence annotations
- Report job can run out of memory
- DeepVariant hangs in rare cases
- ClinVar metadata categorical incomplete
- `_snv.vcf.gz` not published in case of only one chunk
- `.cram` not published in fastq workflow
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