Problem while creating environment from yaml file - iphop iphop Trouble Brewing with YAML Environment Creation Have you encountered a frustrating situation where your YAML file refuses to cooperate when you try to crea 2 min read 05-10-2024 53
How to debug snakemake snakefile in visual studio code? Debugging Snakemake Snakefiles in Visual Studio Code A Step by Step Guide The Problem Snakemake is a powerful workflow management system used for creating compl 2 min read 04-10-2024 46
Setting resources dynamically on snakemake Dynamically Managing Resources in Snakemake Workflows Snakemake is a powerful workflow management system that simplifies complex computational pipelines One key 2 min read 04-10-2024 47
Snakemake wildcard constraint using negative lookbehind or lookahead Understanding Snakemake Wildcard Constraints Using Negative Lookbehind or Lookahead Snakemake is a powerful workflow management system that enables users to cre 3 min read 28-09-2024 55
Snakemake how to move files created to a new directory of same name Moving Files in Snakemake to a New Directory of the Same Name Snakemake is an efficient workflow management system that is particularly useful for bioinformatic 2 min read 23-09-2024 54
fastq-dump.3.1.1 err: item not found while constructing within virtual database module - the path 'SRRXXXXX.sra' cannot be opened as database or table Understanding and Resolving the fastq dump 3 1 1 Error Item Not Found in Virtual Database Module When working with bioinformatics tools particularly in data ret 3 min read 22-09-2024 47
Define input files for snakemake using glob Defining Input Files for Snakemake Using Glob When working with Snakemake a powerful workflow management system one of the common tasks involves specifying inpu 2 min read 22-09-2024 52
Is there a way I can use snakemake to generate files based on sequence in a list? Using Snakemake to Generate Files Based on a Sequence List Snakemake is a powerful workflow management system that allows users to define complex data pipelines 2 min read 20-09-2024 57
Best practices for integrating optional arguments in shell command inside a snakemake pipeline Best Practices for Integrating Optional Arguments in Shell Commands Inside a Snakemake Pipeline Snakemake is a powerful workflow management system that facilita 2 min read 19-09-2024 45
Snakemake: how to produce multiple outputs from one input Snakemake How to Produce Multiple Outputs from One Input Snakemake is a powerful workflow management tool that allows users to define complex data processing pi 3 min read 18-09-2024 47
Snakemake, how to reference input in output of the same rule Snakemake Referencing Input in Output of the Same Rule Snakemake is an innovative workflow management system that enables researchers and data scientists to cre 3 min read 15-09-2024 52
How to Set Exception Rules for Slurm Executor in Snakemake? How to Set Exception Rules for Slurm Executor in Snakemake Snakemake is a popular workflow management system that allows users to define complex data workflows 2 min read 14-09-2024 75
How to deal with paired tumor-normal samples in Snakemake? How to Deal with Paired Tumor Normal Samples in Snakemake When analyzing genomic data particularly in cancer research it is common to have paired tumor normal s 2 min read 14-09-2024 57
config file taking it as literal string snakemake Snakemake The Case of Literal String Configuration Files Sometimes you might want to use a Snakemake configuration file that contains strings exactly as they ar 2 min read 13-09-2024 47
Using Snakemake with sun grid engine array jobs Scaling Snakemake Workflows with Sun Grid Engine Array Jobs Running large scale bioinformatics pipelines with Snakemake on a shared HPC cluster can be a challen 3 min read 05-09-2024 53
Problem while creating environment from yaml file - iphop Solving Encountered problems while solving Errors During Environment Creation When creating a conda environment from a YAML file you might encounter errors like 2 min read 04-09-2024 92
Manage the wrappers in Snakemake Mastering Wrapper Integration in Snakemake A Guide to Seamless Data Flow Snakemakes wrapper system is a powerful tool for streamlining your bioinformatics workf 3 min read 03-09-2024 50
Snakemake: No storage provider found Decoding the Snakemake No Storage Provider Found Error A Deep Dive When working with Snakemake the No storage provider found error can be perplexing This articl 2 min read 02-09-2024 53
How to debug scripts for PyPSA-EUR? Debugging Py PSA EUR Scripts A Deep Dive into Strategies and Solutions Py PSA EUR a powerful tool for analyzing European energy systems relies on Snakemake work 2 min read 02-09-2024 61
Can you order the execution of all expanded jobs in single rule? Prioritizing Snakemake Jobs Ordering Expanded Rules for Efficient Pipelines Scenario You ve got a Snakemake pipeline humming along processing your genetic data 2 min read 31-08-2024 38
Snakemake rule generating symlink in Python script reruns always with "Code has changed" despite no code changes Snakemake Rule Reruns The Mystery of Symbolic Links in Python Scripts Have you ever encountered a Snakemake rule that stubbornly re runs despite no code changes 2 min read 30-08-2024 53
How to enable "output" to detect variables in "run" in snakemake Dynamically Creating Directories in Snakemake using expand and output This article explores a common issue in Snakemake dynamically generating output directorie 2 min read 30-08-2024 81
How to run snakemake on AWS now that Tibanna is not anymore available on Snakemake 8 Running Snakemake 8 Pipelines on AWS A Guide Beyond Tibanna Snakemake a powerful workflow management system has been a popular choice for running complex pipeli 2 min read 30-08-2024 49
How to log time duration (for each job and total) for a snakemake workflow? Tracking Time in Snakemake Workflows Beyond Start Times Snakemake is a powerful workflow management system that streamlines complex computational tasks While it 3 min read 30-08-2024 61
Multiple variables in input and output using wildcards snakemake Handling Multiple Variables with Wildcards in Snakemake A Deep Dive This article tackles a common challenge in Snakemake workflows managing multiple variables w 3 min read 30-08-2024 78