snakemake Examples and Free Source Code

Snakemake "Function did not return str or list of str."...

python function input wildcard snakemake

Can I run a try-except block (or similar) inside a Snakemake rule?...

python shell snakemake

SNAKEMAKE - Missing input files for rule all in snakemake because of wildcard_constraints...

wildcard bioinformatics snakemake

Avoid shell printing output when running in params directive...

shell snakemake

Wrong snakemake glob_wilcards and wildcard_constraints...

python glob snakemake wildcard-expansion

How to use wildcards in keyword wildcard_constraints...

python wildcard snakemake wildcard-expansion

Perl installed via conda snakemake shell error: Can´t open perl script .. no such file or direc...

shell perl anaconda snakemake

Is there a function in snakemake to make the list of output dependent on the arguments passed into t...

python snakemake directed-acyclic-graphs wildcard-expansion

Correctly consuming a multiline config file in snakemake as an input...

python shell yaml snakemake variable-expansion

How to limit usage of disk space in Snakemake?...

python resources priority-queue snakemake diskspace

Prevent rules from rerunning when intermediate file is updated...

python snakemake directed-acyclic-graphs orchestration

Snakemake not recognizing multiple files as input...

python shell yaml bioinformatics snakemake

how to quickly identify if a rule in Snakemake needs an input function...

python wildcard snakemake directed-acyclic-graphs wildcard-expansion

Please explain me why i am getting this error in snakemake? I´ve been strugling for days please...

python pipeline wildcard snakemake rna-seq

Is there a way for Snakemake to evaluate dynamic Snakefile constructs like `eval` does in GNU Make?...

python bash eval gnu-make snakemake

how to speed up task performing using snakemake...

python python-multiprocessing snakemake

conditional target in Snakemake...

python snakemake

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

snakemake

Snakemake 'run' directive produces no error message...

python python-3.x error-handling snakemake

improve snakemake rule in few aspects...

python list-comprehension wildcard snakemake wildcard-expansion

Is a use case for the asyncio package to compute on a set of data while reading the next set from di...

python parallel-processing python-asyncio dask snakemake

snakemake --profile PROFILE_NAME --dry-run results in "No config.yaml found", despite prof...

slurm snakemake hpc

Snakemake scatter-gather with wildcard AmbiguousRuleException...

python wildcard bioinformatics snakemake

Importing local modules into Snakemake files...

python snakemake

How can I define an output that can be either one thing or another in Snakemake?...

python wildcard snakemake

Snakemake: Expand Incorrectly Defining Output Folders...

python wildcard directory-structure snakemake expand

Snakemake: Mismatched Wildcards Variable Values for "output" Rule...

python wildcard directory-structure snakemake cp

Reuse of a rule in Snakemake...

python-3.x snakemake

Snakemake: wildcards do not expand in script line of rule...

wildcard snakemake external-script

Snakemake using the first argument of a list as a wildcard...

snakemake