snakemake

snakemake

InputFunctionException: unexpected EOF while parsing

Snakemake copy from several directories

Snakemake: prevent rerun of subworkflow

lambda function in snakemake output

snakemake list rules to execute in cluster and local

Snakemake problem: Merge all files together with space delimiter instead of iterating through it

Workflow always results in "Nothing to do" even when forcing rules

Using snakemake to copy a file to multiple directories, where a wildcard is used for part of the name of the target

Snakemake: pass command line arguments to scripts

snakemake. How to pass target from command line when creating multiple targets

snakemake job fails if --drmaa-log-dir specified

Snakemake: 'Unexpected keyword notebook in rule definition' when trying to implement Jupyter notebooks

snakemake: copying a file to multiple folders

Snakemake - delete all non-output files produced by a workflow

passing dictionary of wildcard constraints from config file

snakemake batch creation of output

Snakemake variable number of files

Snakemake - Tibanna config support

How to access wildcards within a run directive

Getting wildcard from input files when not used in output files

Snakemake running Subworkflow but not the Rest of my workflow (goes directly to rule All)

Do snakemake-wrappers get fetched once and stored locally? Or fetched everytime from remote URL?

running metabat2 with snakemake but not getting the bin files

How to supply snakemake options within the Snakefile itself?

Combine shell command lines in snakemake

snakemake wildcard scoping between rules

daemons running with workflow?

Snakemake skips multiple of the rules with same input

making snakefile for data analysis

Snakemake add checkpoint output to DAG and report

Snakemake live user input

Snakemake: HISAT2 alignment of many RNAseq reads against many genomes UPDATED

snakemake unpack with shell & conda

Wildcard constraint that does not match a string

Snakemake: HISAT2index buind and alignment using touch

How to add sbatch options such as --wait in a snakemake file

temp() not working on PBS Torque cluster with snakemake

Calling another pipeline within a snakefile result in mising output errors

How to have multiple users run the same pipeline in snakemake - metadata permissions issue

Command not found error in snakemake pipeline despite the package existing in the conda environment

Snakemake with specific combination of files as input

Snakemake & singularity, making different mounts available to each rule

How can I run multiple runs of pipeline with different config files - issue with lock on .snakemake directory

MissingOutputException and latency-wait error with snakemake

Downloading large files from S3 with snakemake

Snakemake: how to specify absolute paths to shell commands

Snakemake: Can you expand on two dependent variables?

Is there a way to create multiple reports (one for each sample say) in a Snakemake worklow

Snakemake: HISAT2 alignment of many RNAseq reads against many genomes

Snakemake “Missing files after X seconds” error

Snakemake wildscard unexpected changed

Snakemake how to execute downstream rules when an upstream rule fails

How are nested checkpoints resolved in snakemake?

How to properly use batch flag in snakemake to subset DAG

Define input files from csv

Including unforeseen file names as wildcards in Snakemake

Snakemake report - Code not displayed in the report

Snakemake files in multiple directories

How to run rule even when some of its inputs are missing?

ChildIOException: error in snake make after running flye

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