MS

ERROR ~ while scanning a simple key

4

### Description of the bug ERROR ~ while scanning a simple key in 'reader', line 3, column 1: 0.4.8 ^ could not find expected ':' in 'reader', line 4, column...

Test+Docker profile fails: "The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine."

5

### Description of the bug ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT ( earlycasualcaiman)' Caused by: Process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman)` term inated with an error exit status (134) Command executed: /opt/deepvariant/bin/run_deepvariant...

Allow multiple unrelated cases/families in samplesheet.csv

1

### Description of feature I have data consisting of several unrelated trios and several individuals. Is it possible to run the pipeline with just one samplesheet (where cases have different...

Option to publish GVCFs

2

### Description of feature Is it possible to publish GVCF file for every sample?

Test+Docker profile fails: "ValueError: `call_variants_outputs` did not pass sanity check."

1

### Description of the bug Aug-12 14:30:26.359 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat)' Caused by: Process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat)` terminated with an error exit status (1) Command...

GATK4_HAPLOTYPECALLER not running in parallel

10

### Description of the bug As a minimal example, I am locally (on a system with 24 cores and 128 GB RAM) running joint germline with just two WES samples...

Order of samples in family SNV and SV VCFs is different

1

I am doing trio analysis, and noticed that the order of sample names in call_sv/genome/${FAM}_sv.vcf.gz and call_snv/genome/${FAM}_snv.vcf.gz is different, what causes small problems in my downstream analyses. It would be...

I am doing WES analysis with regions specified with --target_bed, but I do not see any mosdepth coverage report per region (only per chromosome and per base). Is it a...

Within the conda environment, the command parascopy pretable --force --fasta-ref ref.fa --output pretable.bed.gz is not able to find bedtools. Probably it is not installed in the environment.