snakemake

snakemake

Snakemake: a rule with batched inputs and corresponding outputs

snakemake checkpoint and create a expand list/wildcards based on created output files

How do Snakemake checkpoints work when i do not wanna make a folder?

Snakemake Megahit output issue

Multiple users executing the same workflow

snakemake: define parameter based on sample name or other input

snakemake RuleException, if run command in CLI, work well; but if run in snakemake, failed;

Snakemake explicit handling for Out Of Memory (OOM) failures

Split multiple files into multiple parts with Snakemake

Error when running cwl wrapper from documentation

Dynamic Branching/Plumbling

Snakemake cluster mode with different CPU count for each rule

Automatically run rule when file changes in Snakemake

Snakemake: Data-dependent conditional execution of rules, IndexError

Snakemake: catch output file whose name cannot be changed

Is it possible to have optionally empty Snakemake wildcards?

How to implement splitting of files in snakemake when number of files is known

Using * to glob within an input file, or using multiple wildcards in input, then using only one wildcard for output?

Snakemake How to design downstream rules on empty output files?

How to avoid Snakemake rule from using incomplete output file from other rules

No module named 'nbformat.v1.convert' error for Snakemake rule

Snakemake: What will happen if the output file of a rule is already generated?

AmbiguousRuleException when there is no ambiguity

How to use Snakemake for memory management?

How to pass a list or dictionary using Snakemake's command line config option

How to target intermediary Snakemake rule that contains wildcards

Refer to input or output files of another Snakemake rule

setting FTP proxy with snakemake FTP provider

Iterate over 2 parameters in a Snakemake rule

Split files in Snakemake

snakemake - Missing input files for rule salmon_quant: error

Snakemake input two variables and output one variable

snakemake randomly identifying outputs as incomplete

Running external scripts with wildcards in snakemake

snakemake - define input for aggregate rule without wildcards

snakemake - replacing command line parameters with wildcards by cluster profile

Try using sample Group info Encounter AttributeError about module 'pulp'

Accessing the --default-remote-prefix within the Snakefile

use directories or all files in directories as input in snakemake

Keep Snakemake jobscript after a failed cluster execution?

How does snakemake know files created though a slurm job are incomplete when job is canceled?

STAR snakemake wrapper with configfile

Snakemake: output files in one output directory

Snakemake-Wildcards in input files cannot be determined from output files

Can a snakemake job mistakenly run twice at the same time?

snakemake "rule all" is rerunning unnecessary rules

Snakemake : subworkflow not playing well with the main DAG

Possible to have wildcard as dictionary key in snakemake rule output?

Sample Input from file

Is there any way to access the --cores argument in a snakemake workflow?

Discard part of filename in Snakemake: "Wildcards in input files cannot be determined from output files"

Snakemake expand function alternative

Using SnakeMake, how to pass SLURM flags with dashes in their names?

How to avoid "missing input files" error in Snakemake's "expand" function

Snakemake: wildcards for parameter keys

snakemake rule won't run the complete command

How to change the output directory in Snakemake without using cd

Error in Snakemake 'Unexpected keyword expand in rule definition'

Snakemake: Combine cluster profile with resources: attempt

Change the directory name and fastq file name with snakemake

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