Felix Mölder

snakefmt adds wrong indentation

7

It looks like `snakefmt 0.4.4` adds wrong indentations when formatting a snakemake rule containing a if-else-closure. As an example the following output will be created for a proper formatted rule:...

When performing primer trimming with single primers I noted that improper paired reads are always trimmed by the maximum primer length even if a primer can be assigned to one...

### Description A wrapper for datavzrd ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced...

Update rust-bio-tools to 0.41

1

Try building rust-bio-tools for macOS 10.14

For large samples `fgbio AnnotateBamWithUmis` fails due to memory issues. This happens as fgbio loads the fully uncompressed UMI fastq file into memory. We already tried to fix this in...

This PR changes the header number from `Number=A` to `Number=.` for dbNSFP entries. This fixes the bug described in issue [36](https://github.com/pcingola/SnpSift/issues/36)

For annotation AlphaMissense scores with VEP scores need to be downloaded and index first. This has been a manual step before. To improve this further scores are now download from...

This adds `vg giraffe` for mapping reads as bam records. Like for `bwa mem` sorting reads by samtools, picard or fgbio is supported. ### QC * [x] I confirm that...

fix: fix short observation plot

1

Short observation plots were not shown anymore due to a type error. Somehow this error occurred since updating to a newer datavzrd wrapper version. ## Summary by CodeRabbit - **New...

feat: samtools_opts for picard markduplicates

1

This allows to pass samtools parameters to the wrapper allowing to e.g. specify the cram version created by samtools. Doing so might be necessary as some tools like GATK and...