Leandro Hermida

Apologies if I've missed where it is in the API, but I cannot find how to specify querying a previous GDC data release version.

Option to control gzip output compression level

2

Currently seqkit fixes the gzip output compression level to 5. Would be nice to provide an option to control gzip output compression level between 1-9

Rules downstream of a checkpoint aggregation rule keep being re-executed even when all output files exist and nothing upstream has changed

16

**Snakemake version** 7.12.1 **Describe the bug** Rules downstream of a `checkpoint` aggregation rule are always re-executed when both aggregation and downstream rules have already been run and output files exist....

`glob_wildcards` doesn't support specifying same wildcard in more than one place in path

1

There are definitely use cases when you have data where e.g. the directory has the same name as the beginning of the files within the directory, and with regular rules...

Option to increase prefetch size of jobs ready to execute

1

**Is your feature request related to a problem? Please describe.** Not specifically, other than improving performance. One of my rules needs to execute for 20k+ files, and `Select jobs to...

Please add ggvenn to conda-forge, it would get a lot more users and people could better integrate into their environments and software dists

ridgeplot showCategory doesn't accept vector of specific pathways

2

```R library(clusterProfiler) library(msigdbr) data(geneList, package="DOSE") C3_t2g % dplyr::select(gs_name, entrez_gene) em2

Output unmapped reads to FASTQ names file (like Salmon `--writeUnmappedNames` feature), alignments SAM file, or FASTQ files

The initial fixFasta step of Pufferfish indexing is single-threaded, and when there are a lot of sequences in the reference it takes a lot of time. From the outside it...

Speed up `search` channel loading performance

4

Mamba has done an excellent job of gradually replacing conda commands with high performance versions. A remaining one is `search`. Channel loading is very slow (uses conda still) and it...