snakemake

snakemake

Snakemake tabular configuration, expand, and merge - how to expand input files correctly?

Snakemake: Exchanging variables

How do I get Snakemake to apply all samples to a single rule, before proceeding to the next rule?

Is it possible in snakemake to produce reports and the DAG images automatically?

Working directory when using include in snakemake for rules that use the report() function

Snakemake wrappers fails to open environment file: HTTP Error 404: Not Found

Using the expand() function in snakemake to perform a shell command multiple times

Snakemake shell command should only take one file at a time, but it's trying to do multiple files at once

Snakemake always rebuilds targets, even when up to date

snakemake running single jobs in parallel from all files in folder

Include Parameters and source code in Snakemake HTML Report

output of one rule as input of another

Is there a way to get a nice error report summary when running many jobs on DRMAA cluster?

Wildcard SyntaxError in Snakemake with no obvious cause

snakemake with prefix as output including a path

Snakemake: The use of --debug-dag for detecting cyclic dependencies

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

Is it possible to return a rule by a function in Python Snakemake?

Snakemake: variable that defines whether process is submitted cluster job or the snakefile

Snakemake read input from file

snakemake --use-conda with an already created envs

ImproperOutputException in snakemake 5.5.4

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

shell() function in run does not use singularity

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

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

split bam files to (variable) pre-defined number of small bam files depending on the sample

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

NameError Snakemake when I want to run my code [duplicate]

Subworkflow as an implicit dependency

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

How to ensure snakemake rule dependency while submitting via qsub

Does Snakefile location matter?

Snakemake - input function exception

Snakemake › Access multiple keys from config file

ambiguousruleexception in snakemake, parms crash of two branches

Use of Snakemake workflows in AWS Batch

Conditional execution of multiplexed analysis with snakemake

Can I have the output as a directory with input having wildcards in Snakemake? To get around jobs that fail and force rule order

Snakemake subworkflow result is not found if I specify a target in subfolder

always report errors: 'str' object is not callable in my snakemake for RNA-seq workflow

Snakemake: Is it possible to only display "Job counts" using --dryrun?

How to run only one rule in snakemake

Wildcards in input and output not working

snakemake: how to implement log directive when using run directive?

snakemake: write files from an array

How to add to a config file within a snakemake pipeline and define global variables?

Snakemake: Use the value of another expand variable in declaration

Snakemake : "wildcards in input files cannot be determined from output files"

snakemake rules: Passing on variables outside of the file name

How to pass variable value as input in snakemake?

How to output the shell script even after all the rules have been finished in `snakemake`?

wildcard_constraints between two wildcards with OR

A curious case of snakemake

Snakemake grouping output

Is there a way to get the config file name specified by --configfile?

Aggregate undetermined number of files for all wildcards in one rule

Snakemake rule is run only for one file

Snakemake: strip off path from input

snakemake: correct quoting when using singularity

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