snakemake

snakemake

How to run only one rule in snakemake

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

how to do dynamic input for all rule with checkpoint wildcards, for a rule that uses wildcards in input and output

Wildcards in input and output not working

Snakemake - Google Cloud Preemptible instances

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

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

Obtain actual --cores [N], --jobs [N], -j [N] value given from command line within the snakefile

Snakemake cluster command with mem_mb resources in multiple cluster environments (LSF, SGE)

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

Can snakemake create job error and output files automatically on a SLURM cluster?

Snakemake: Use the value of another expand variable in declaration

Aggregate undetermined number of files for all wildcards in one rule

How to prevent snakemake from deleting output folders from failed jobs?

Snakemake : “wildcards in input files cannot be determined from output files”

How to determine failed rule in “onerror”?

How to fix 'MissingOutputException'?

snakemake rules: Passing on variables outside of the file name

How to get access to the snakmake options inside the Snakefile

snakemake temp() causing unnecessary rerun of rules

The touch of death

How to indicate variable node-local-storage paths to snakemake using --shadow-prefix?

Snakemake grouping output

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

Snakemake: strip off path from input

Snakemake rule is run only for one file

wildcard_constraints between two wildcards with OR

How to pass variable value as input in snakemake?

A curious case of snakemake

snakemake + singularity, getting rid of python dependency

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

Access jobid inside cluster.yaml file

snakemake: correct quoting when using singularity

snakemake script access to stdin / stdout for stream processing

How to fix 'File name too long' errors when using Snakemake

The 'conda' command is not available

Parallel execution of a snakemake rule with same input and a range of values for a single parameter

Run one rule conditionally to the input files

Syntax for merging technical replicates in Snakefile and config file

Is there a way to set parameters for the Java VM when using a Snakemake wrapper?

define alternative rules with snakemake

snakemake define folder as output

Recursive input calling in Snakemake rule

Snakemake: STAR fails in snakemake but not standalone

Install older version of snakemake

Snakemake Combine analysis of different input types in one workflow

Snakemake and STAR

Can I add a file to rule all: which is not defined in output

Getting data from iRODS server from snakemake

Snakefile ValueError: need more than 1 value to unpack

Snakemake to --export-cwl conversion requires static config/inputs

Snakemake how to set qsub ppn per task?

How do I make the benchmark directive contain mem usage on macOS?

Rules with shared shell section

Printing simplified DAG plot with snakemake

Adding conditional in a snakemake wrapper shell section

Snakefile and wildcard/regex for Output file naming

limit total thread use, number of jobs, and maximum threads per rule when using qsub with snakemake

Summarize snakemake steps singly: one per rule in Snakefile

snakemake substitution issue

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