snakemake-wrappers

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fix: gffread issue with reading gff files, writing fasta files

1

The gffread wrapper raises `ValueError: Unknown annotation format` for gff files. In addition to this, the wrapper assumes that any fasta output contains the spliced exons of each transcript (produced...

nikostr

**Describe the bug** Some programs have changed version type (e.g. #3286), leading to older versions being installed. In this case, the oldes versions is `2013` while the newest is `1.4.1`,...

fgvieira

chore: release 4.7.6

1

:robot: I have created a release \*beep\* \*boop\* --- ### [4.7.6](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.7.5...v4.7.6) (2024-10-25) ### Performance Improvements * autobump bio/kallisto/quant ([#3090](https://www.github.com/snakemake/snakemake-wrappers/issues/3090)) ([a9b8030](https://www.github.com/snakemake/snakemake-wrappers/commit/a9b80301d09711893d74fdba1d0d17b651ced80a)) * autobump bio/last/lastal ([#3363](https://www.github.com/snakemake/snakemake-wrappers/issues/3363)) ([9cd89b2](https://www.github.com/snakemake/snakemake-wrappers/commit/9cd89b29dbb9ab07e41a427c10c688ff029017f3)) * autobump bio/last/lastdb ([#3362](https://www.github.com/snakemake/snakemake-wrappers/issues/3362)) ([0181ce5](https://www.github.com/snakemake/snakemake-wrappers/commit/0181ce5238aee173040723b2e265b7a0301490a6))...

github-actions[bot]

perf: autobump bio/rubic

1

Automatic bump of bio/rubic.

snakedeploy-bot[bot]

perf: autobump bio/reference/ensembl-biomart-table

1

Automatic bump of bio/reference/ensembl-biomart-table.

snakedeploy-bot[bot]

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...

FelixMoelder

Having a stale bot does not make issues go away, and just hides them the longer they have been unresolved, which is kind of the opposite of what should happen......

lczech

feat: create nanosim wrapper for all three modes of simulator.py

7

respective tests already passed locally ### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly...

dlaehnemann

feat: added wrapper for Paraphase

16

Paraphase by PacBio, takes HiFi aligned BAMs as input and phases haplotypes for genes of the same family, determines copy numbers and makes phased variant calls. ### QC * [x]...

MagdalenaZZ

Custom meta-wrappers

3

**Is your feature request related to a problem? Please describe.** There is no documentation [here](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#meta-wrappers) or [here](https://snakemake-wrappers.readthedocs.io/en/stable/meta-wrappers.html) on custom meta-wrappers. From source, it appears meta-wrappers cannot be sourced in the...

t-silvers