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Questions tagged [snakemake]

Snakemake is a workflow management system with a Python-style specification language.

Snakemake is a workflow management system with a Python-style specification language.

1634 questions
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making snakefile for data analysis

I am making a Snakefile for data analysis. the extension of my raw data is .RCC. for example the first input file I have is: CF30207_01.RCC. and the script I am running on the data is QC.py. Looking at the tutorial, I have made the following…
user10657934
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Snakemake with Singularity

I'm trying to use Singularity within one of my Snakemake rules. This works as expected when running my Snakemake pipeline locally. However, when I try to submit using sbatch onto my computing cluster, I run into errors. I'm wondering if you have any…
ksw
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Snakemake add checkpoint output to DAG and report

What I currently want to get going is, to add all the files created in "someDir/" to my DAG and add them to my report. The problem is mainly that those files are created in the checkpoint, thus I can't define them as wildcards beforehand. The…
Noob
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How to export conda env after installing packages using pypy3, to be used with snakemake

I'm using snakemake with conda env. I created conda environment like conda create -n myenv some_packages after that I used pypy3 to install other packages, like. pypy3 -m some_package pypy3 -m pip install --no-cache-dir some_package Now I exported…
Medhat
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Snakemake Wildcards SyntaxError

I know this is a common error and I already checked other posts but it didn't resolved my issue. I would like to use the name of the database I use for SortMeRNA rule (rRNAdb=config["rRNA_database"]) the same way I use…
Elysire
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Snakemake: HISAT2index buind and alignment using touch

Following my previous question:Snakemake: HISAT2 alignment of many RNAseq reads against many genomes UPDATED. I wanted to run the hisat2 alignment using touch in snakemake. I have several genome files with suffix .1.ht2l to…
user3224522
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execute snakemake rule as last rule

I tried to create a snakemake file to run sortmeRNA pipeline: SAMPLES = ['test'] READS=["R1", "R2"] rule all: input: expand("Clean/4.Unmerge/{exp}.non_rRNA_{read}.fastq", exp = SAMPLES, read = READS) rule unzip: input: fq =…
Arun
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Snakemake: HISAT2 alignment of many RNAseq reads against many genomes UPDATED

I have several genome files with suffix .1.ht2l to .8.ht2l bob.1.ht2l ... bob.8.ht2l steve.1.ht2l ... steve.8.ht2l and sereval RNAseq samples flower_kevin_1.fastq.gz flower_kevin_2.fastq.gz flower_daniel_1.fastq.gz flower_daniel_2.fastq.gz I…
user3224522
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Snakemake: RuntimeError stack trace missing when using Python fileConfig()

I have a snakefile with one rule which imports a local Python script and then raises a RuntimeError. When I run the snakefile, the stack trace for the RuntimeError is not shown. The code and snakemake output are shown below. // test.snakefile rule…
mmy227
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Calling another pipeline within a snakefile result in mising output errors

I am using an assembly pipeline called Canu inside my snakemake pipeline, but when it comes to the rule calling Canu, snakemake exits witht he MissingOutputException error as the pipeline submits multiple jobs to the cluster itself so it seems…
Lamma
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temp() not working on PBS Torque cluster with snakemake

When I define an output/input file with temp(), the file does not seemed to be removed when running on a PBS Torque cluster. Is this a known problem? if so is there a workaround? or a maybe a way to write a rule to remove a file when it is no longer…
awitney
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Snakemake: HISAT2 alignment of many RNAseq reads against many genomes

I have several genome files, all with suffix .1.ht2l to .8.ht2l bob.1.ht2l bob.2.ht2l bob.3.ht2l bob.4.ht2l bob.5.ht2l bob.6.ht2l bob.7.ht2l bob.8.ht2l steve.1.ht2l ....steve.8.ht2l and so on and sereval RNAseq samples,…
user3224522
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Snakemake with specific combination of files as input

Do you know how to run snakemake with specific combination of files? i.e. In this txt files I have list of sequence ID's: bob.txt steve.txt john.txt From these files I want to extract the sequences of the ID's in the above…
user3224522
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Downloading large files from S3 with snakemake

I am making a workflow in snakemake 5.8.2 which takes as an input huge files from S3 (280Gb each of 4 files). The first rule just concatenates the files. When I run the workflow, it seems to download only 5GB of some split version of each file,…
ilyavs
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How to run rule even when some of its inputs are missing?

In the first step of my process, I am extracting some hourly data from a database. Because of things data is sometimes missing for some hours resulting in files. As long as the amount of missing files is not too large I still want to run some of the…
Jan van der Laan
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