diff --git a/README.md b/README.md index c8c3f10342b32d2ec4baae0b92b133cf7b9d83c0..0dd0a881e08cb9ec078dec9fdb14daa899fc30f8 100644 --- a/README.md +++ b/README.md @@ -369,8 +369,6 @@ nohup snakemake --profile SUBMIT_CONFIG/slurm/ & ``` --- - - ## More Useful Tips The user can directly override any of the Snakemake parameters (and paths) set in the respective configuration files through the command line when executing GEP. For example, to override the values in the sample configuration [GEP/configuration/config.yaml](configuration/config.yaml) for the path to the main results folder without having to edit the document itself: @@ -398,6 +396,16 @@ snakemake --profile SUBMIT_CONFIG/default/ --until <ruleName> In such cases all files that this rule depends on will be run, but final PDF reports will not be created. +--- +## Known issues + +There is a known merqury issue where png k-mer plots are not generated, making the pieline to fail. If this happens to you, please use this fix: +1. Go to the gep installation folder. +2. Run the following command: +``` +VAR=$(grep merqury .snakemake/conda/*.yaml | awk -F'[:/.]' '{print $4}'); sed -i '/function check_module()/,/^}/s/echo \$?/echo 1/' .snakemake/conda/${VAR}/share/merqury/util/util.sh +``` + ### ERGA Assembly Reports If you are evaluating a pre-curation and post-curation steps, you can obtain the yaml file automatically filled to produce an ERGA Assembly Report (EAR). Please run like this: