David Koppstein

fix: set number of cores for GenericClusterExecutor and DRMAAExecutor to cores rather than None (i.e. all)

2

set number of cores for GenericClusterExecutor and DRMAAExecutor to cores rather than None (which defaults to all) ### Description This pull request passes the --cores parameter to the GenericClusterExecutor and...

convert workflow.included to list of strings

1

This is a simple fix of #33 to convert the workflow.included object into a list of strings.

enable spikein GTFs for mRNA-seq featureCounts

2

We recently came across the issue where the spikein GTF as specified using createIndices is not considered when using featureCounts in the mRNA-seq pipeline.

--singularity-args quotes not propagated to cluster job script

1

**Snakemake version** 8.11.3 Also using: * snakemake-executor-plugin-lsf=0.2.4 * snakemake-executor-plugin-jobstep=0.1.10 * snakemake-interface-common=1.17.2 * snakemake-interface-executor-plugins=9.1.1 **Describe the bug** When running snakemake with e.g. `--use-singularity --profile lsf_plugin --singularity-args "-B /tmp,/home/david"`, the quotes around...