Questions tagged [snakemake]
Snakemake is a workflow management system with a Python-style specification language.
snakemake
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How Do I Combine Parameters Conditionally?
Suppose I have the following input FASTQ files:
$ ls -1 inputs/
CM0009619-ABB_L01_Read1_Sample_Library_XY102.fastq.gz
CM0009619-ABB_L01_Read1_Sample_Library_XY110.fastq.gz
CM0009619-...
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Snakemake running as an AWS Batch or an AWS Fargate task raises MissingInputException on the inputs stored on a S3 bucket
We have a Dockerized Snakemake pipeline with the input data stored on a S3 bucket snakemake-bucket:
Snakefile:
rule bwa_map:
input:
"data/genome.fa"
output:
"...
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Missing Output Exception Error in Snakemake with output directory modified
I'm trying to run a workflow on snakemake. I have to automate a couple of steps which are depending all on python scripts or pipelines already made. My rule Gene_flow_between _species has to run once ...
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Missing Output Exception Error in Snakemake with output directory
I'm trying to run a workflow on snakemake. I have to automate a couple of steps which are depending all on python scripts or pipelines already made. My rule Gene_flow_between _species has to run once ...
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Multiple variables in input and output using wildcards snakemake
rule all:
input:
expand("tissues/{id}/atac_seq/{srr}/{srr}_S1_L001_R1_001.fastq.gz", id =IDs, srr = df[df['library_type']=='Chromatin Accessibility']['Library']),
expand("...
- 45
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How to log time duration (for each job and total) for a snakemake workflow?
If I run a snakemake workflow, the start time for each job is logged to the console, for example
[Fri Jul 12 10:39:15 2024]
How can I adapt the logging to also show the duration for each job and the ...
- 11.6k
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How to run snakemake on AWS now that Tibanna is not anymore available on Snakemake 8
Currently I am running snakemake pipelines on AWS using an older version of Snakemake (7.30.0). I would like to update to a more recent version of Snakemake. Unfortunately it seems that Tibanna is not ...
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How to enable "output" to detect variables in "run" in snakemake
I am trying to make directories for the different "IDs" I have stored in the .csv file (they are stored under column "ID"). However, snakemake doesn't seem to be able to detect &...
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Snakemake rule generating symlink in Python script reruns always with "Code has changed" despite no code changes
I have a snakemake rule that generates symbolic links in a target folder. This is done within a Python script and the script directive in the rule. This rule is always rerun with reason: Code has ...
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Can you order the execution of all expanded jobs in single rule?
I have a snakemake pipeline that runs a genetic analysis. The genome has been split into many 'regions'. These regions can run in parallel, and therefore I've used expand(), and they all run as ...
- 1,024
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config file taking it as literal string snakemake
shell:
"""
cellranger-arc count --id={wildcards.atac_srr}_{wildcards.rna_srr} \
--reference={config['path']['ref_genome']} \
--...
- 45
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37
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How to deal with paired tumor-normal samples in Snakemake?
I am converting a bash pipeline to process paired whole-exome sequenced tumor-normal samples into a SnakeMake workflow.
Paired samples are listed in my config file, as follows:
sample_list:
- sample:...
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How to Set Exception Rules for Slurm Executor in Snakemake?
I am currently working with a Slurm workload manager to manage and schedule jobs on our cluster. While most of my tasks are submitted and managed by Slurm, I have a few specific tasks that I would ...
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Snakemake, how to reference input in output of the same rule
My logic is probably flawed here, and I need your help to get the best possible approach to solving this:
I have a daisy-chained workflow where I annotate a .vcf file in multiple steps, and each step ...
- 457
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How to debug scripts for PyPSA-EUR?
I would like to set some VisualStudioCode or PyCharm breakpoints for the script
https://github.com/PyPSA/pypsa-eur/blob/master/scripts/prepare_sector_network.py
and then run and debug it to better ...
- 11.6k