I am new to Snakemake and planning to use Snakemake for qsub in my cluster environment. In order to avoid critical mistakes that may disturb the clust ...

I get an annoying write error during a pipeline execution which shutdown everything and cannot understand the reason. I don't know whether this is a b ...

In my workflow, I wish to run some rules based on different wildcards. I have a {group} wildcard, which is derived from a directory, and a {sample} wi ...

I am new to Snakemake, I just started using it for my project. I am trying to run a software package that uses Snakemake, however the workflow fails a ...

When I run jobs on snakemake using --profile ./slurm, I see in standard output: in slurm/config.yaml I have: This writes log files like 406.err ...

I've stuck on this problem for several days. I created environment envs/jupyter.yaml as followed the snakefile rules looks like When I run "sna ...

I have 3 rules and their names are somewhat long. When using ruleorder, the line goes over my desired 80 character limit. Is it possible break up the ...

I'm trying to run the following snakemake workflow: https://github.com/snakemake-workflows/rna-seq-star-deseq2 . I tried different virtual environment ...

I use the snakemkae to create a pipeline to split bam by chr,but I met a problem, Wildcards in input files cannot be determined from output files: 'Ou ...

I have a rule that contains a wildcard that is taken from the params (decided by a function). Is it possible to run this single rule by calling it by ...

Is there any standard or recommended way to add a version number to a pipeline (written in snakemake in my case)? For example, I have this pipeline a ...

I am running a Snakemake NGS data analysis pipeline, one rule uses Freebayes, it's env looks like this: name: freebayes channels: - bioconda depend ...

I am getting an MissingOutputException from my snakemake workflow, snakemake creates the required output in the desired directory but keeps looking fo ...

So I know that in order to set rule priority, you use ruleorder. Is there an efficient way to give a rule priority over all other rules? For example, ...

Would it be possible to have a wildcard that could be empty in the output file and in the same time, the rule can be run by calling the rule name? By ...

How can we define specific config files for includes in snakemake workflows? I have a pipeline with the following structure. The main entrypoint of ...

I am trying to include a report of my Snakemake (7.18.2) workflow using the automated snakemake --report functionality. However, I find the styling of ...

My directory structure looks like this: I would like to create a rule which aggregates information of all files which carry the time_average name, ...

. Answers to this question are eligible for a +50 reputation bounty. so ...

I have what I hope is a simple question. I have been working on a Snakemake pipeline, for which I would like to add a config flag for if the pipeline ...