add snakemake workaround

README.md

@@ -11,6 +11,9 @@ The manuscript is available in [Nature Protocols](https://www.nature.com/article
 
 
 ## What's new
+
+`Snakemake v.7.8` introduced some changes in which changes in parameters can cause rules to be executed. More info [here](https://github.com/snakemake/snakemake/issues/1694). This affects DROP and causes certain rules in the AS and QC modules to be triggered even if they were already completed and there were no changes in the sample annotation or scripts. The workaround is to run DROP adding the parameter `--rerun-triggers mtime`, e.g. `snakemake -n --rerun-triggers mtime` or `snakemake --cores 10 --rerun-triggers mtime`. We will investigate the rules in DROP to fix this.
+
 Version 1.2.2 fixes some critical bugs that affected the performance of the `aberrantExpression` pipeline, and allows sample IDs to be numeric.
 
 As of version 1.2.1 DROP has a new module that performs RNA-seq variant calling. The input are BAM files and the output either a single-sample or a multi-sample VCF file (option specified by the user) annotated with allele frequencies from gnomAD (if specified by the user). The sample annotation table does not need to be changed, but several new parameters in the config file have to be added and tuned. For more info, refer to the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#rna-variant-calling-dictionary).