Snakemake issues running rules on two different subsets of wildcards...

Snakemake - dynamically derive the targets from input files...

Snakemake: 'Missing input files' due to wrong wildcard expansion...

Snakemake read input from file...

Put optional input files for rule all in Snakemake...

How can I run a subset of my snakemake rules several times with wildcards?...

snakemake substitution issue...

Preventing input function from generating files not present in sample file...

Snakemake: Is it possible to use directories as wildcards?...

split bam by clusters and then merge bam by cluster using checkpoint...

How to perform simple string operations in snakemake output...

How to stop snakemake from adding non file endings to wildcards when using expand function? (.g.vcf ...

calling variables for rule individually and adding an independent environment for a specific rule...

How to get a rule that would work the same on a directory and its sub-directories...

How to use output directories to aggregate files (and receive more informative error messages)?...

How to handle mutliple output filename conventions with Snakemake...

Snakemake how to ignore a RuntimeWarning?...

--latency-wait Error MissingOutputException...

Snakemake - How to use every line of input file as wildcard...

snakemake: Run some tasks on cluster and some locally...

How to fix conda "ResolvePackageNotFound" when building a conda recipe...

Can a snakemake input rule be defined with different paths/wildcards...

How to ensure snakemake rule dependency while submitting via qsub...

Building a workflow with dynamic input without using deprecated dynamic API...

How to access variables defined in the snakefile in a snakemake wrapper?...

Is it possible to have an optional output file in Snakemake?...

Snakemake complains it can't find the file it is supposed to create in a run instruction...

Executing checkpoint intermediate Commands...

snakemake PICARD merge bam files...

How do I get a snakemake rule to execute M times to generate MxN files?...