Lucas Czech

Group name "Hidden" shows up in help

1

According to https://cliutils.github.io/CLI11/book/chapters/options.html, the group name "Hidden" should lead to the options in that group not being shown in the help. However, with CLI11 v1.9.1, they still show up. I...

Given a FASTA file with unaligned sequences, when calling with `--msa file.fasta`, without specifying `--msa-format FASTA`, the error message is ERROR: Error loading MSA: cannot parse any format supported by...

hts_log_error() extension for better error reporting

5

Hi there! This is more of a general suggestion to improve error reporting, but I'll illustrate it with a concrete example. I have started using the sam/bam/cram functionality recently, and...

Phasing of first genotype

5

Hi there, according to the VCF Spec 4.2, > For one individual, **each integer** in the vector is organized as `(allele + 1)

Multiple strings in FORMAT fields

2

This is a variation/duplicate of https://github.com/samtools/htslib/issues/664, which I could not re-open, hence please excuse to start a new issue here. The above issue handles the case of setting variable length...

VQSR not fully implemented

4

It seems that the VQSR (GATK VariantRecalibrator) step [here](https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/cffa77a9634801152971448bd41d0687cf765723/workflow/rules/filtering.smk#L29-L39) is not fully implemented. That rule only produces the model built with the [VariantRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360050815872-VariantRecalibrator), but does not use [ApplyVQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360036431392-ApplyVQSR) to actually...

bwa-mem2 incorrect index

6

The [wrapper 1.7.0 for bwa-mem2](https://snakemake-wrappers.readthedocs.io/en/v1.7.0/wrappers/bwa-mem2/mem.html) contains the following code: ```.py index = snakemake.input.get("index", "") if isinstance(index, str): index = path.splitext(snakemake.input.idx)[0] else: index = path.splitext(snakemake.input.idx[0])[0] ``` which mixes `index` and `idx`,...

picard CollectMultipleMetrics missing output files

1

**Snakemake version** Snakemake 5.31.1 Wrappers 0.74.0 **Describe the bug** After running the [picard CollectMultipleMetrics](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html) wrapper, some output files might be missing if the input files were too small for picard...

vep download cache: Add cache url

3

**Is your feature request related to a problem? Please describe.** The documentation of VEP makes it not very obvious how to use genomes that are not Homo sapiens, and it...

vep download cache vs vep annotate

3

**Snakemake version** snakemake-wrappers: 0.74.0 **Describe the bug** The [vep download cache](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/vep/cache.html) wrapper uses the vep_install `--AUTO cf` mode, which downloads the cache _and_ fasta data. However, the [vep annotate](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/vep/annotate.html) wrapper...