snakemake

snakemake

Running different snakemake rules in parallel

How to reference input in params section of snakemake rule?

Using a reference genome not on ensembl for Snakemake?

Is it possible to see qsub job scripts and command line options etc. that will be issued by Snakemake in the dry run mode?

Random "[Errno 13] Permission denied" during snakemake pipeline execution on cluster

what is the snakemake variable name for slurm job id?

MissingOutputException snakemake

Snakemake, producing list of files that are created within the pipeline

Honour module's `config.yml` when dynamically importing modules into Snakemake workflow

Snakemake pipeline not attempting to produce output?

Snakemake combine ambiguous rules

"scancel: error: Invalid job id Submitted batch job" with --cluster-cancel from snakemake

Snakemake: Only input files can be specified as functions

How to use include directives with specific config files in snakemake?

Getting snakemake environment variables local to a compute node in cluster execution

Function to determine path from imported module output

Bcftools 1.16 able to add F_MISSING tag?

Snakemake - Using config file when having multiple inputs per sample

Why is no AmbiguousRuleException raised with these Snakemake rule and output combinations?

Snakemake - MissingInputException

Input function for technical / biological replicates in snakemake

Can I use snakemake with humans-in-the-loop?

Snakemake: Solving dependencies between modules

Delete unwanted Snakemake Outputs

Have Snakemake recognize complete files upon relaunch

Wildcard constraints scope not used by modules

Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile

Does Snakemake have states during a workflow

snakemake wrapper Gatk/Mutect2

Using multiple config file in snakemake results in not same wildcard error

Relative Directories in snakefile using workflow.get_source()

snakemake output files as list/table

Can Snakemake parallelize the same rule both within and across nodes?

How does the --touch flag for snakemake work exactly?

Containerization of Conda based workflows

Modularization: Use config.yaml file from GitHub repository for module

snakemake rule error. How can I select rule order?

Snakemake checkpoint output unknown number of files with no subsequent aggregation but instead rules that peform actions on individual files?

How to efficiently combine N files, two at a time

snakemake dry run for a single wildcard in order of execution

Snakemake using the first argument of a list as a wildcard

how to add "wildcard-specific wildcard" via snakemake checkpoint

snakemake if else statement within rule input

Deterministic colors for Snakemake --dag/--rulegraph output

snakemake returns a non-zero exit status on a simple rule when executing with --cluster

Way to force snakemake to re-evaluate dag before checkpoint with --list-input-changes?

How to update output files without changing them in Snakemake

Why is my snakemake rule with wildcards turned into a localrule?

Snakemake MissingInputException

add `shell.prefix()` in snakemake profile?

Use wildcard in python shell rule

How does snakemake handle possible corruptions due to a rule run in parallel simultaneously appending to a single file?

Named rules and local rules

Snakemake: Pass all wildcards to a single shell command

Access snakemake expand-ed variables in a script

Interconnected variables in snakemake

How to write a Snakemake rule with no output?

Snakemake is unable to match wildcard although it's defined and even suggested

Erroneous MissingOutputException errors on Google Cloud/Kubernetes

Snakemake Error with MissingOutputException

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