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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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Force a certain rule to execute at the end

My question is very similar to this one. I am writing a snakemake pipeline, and it does a lot pre- and post-alignment quality control. At the end of the pipeline, I run multiQC on those QC results. Basically, the workflow is: preprocessing -> fastqc…
luomengt
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Using R in a Snakemake workflow with Mambaforge

I'm building a pipeline with Snakemake. One rule involves an R script that reads a CSV file using readr. I get this error when I run the pipeline with --use-singularity and --use-conda Error: Unknown TZ UTC In addition: Warning message: In…
Tomas Bencomo
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How to start a Snakemake workflow on AWS and detach?

I am trying to execute a Snakemake workflow on AWS, and have succeeded in executing my workflow using the command: snakemake --tibanna --use-conda --default-remote-prefix=mybucket/myproject and it works successfully. So far, so good. Unfortunately…
Muhammad Alkarouri
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Snakemake perform rules based on configs

I wish to do be able to write a workflow so that I can choose which optional rules to run in the config.json file. For example if I have a Snakefile with 2 rules, rule_a and rule_b, each with the same input but different outputs: rule_a: input:…
user9367574
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Execute certain rule at the very end

I am currently writing a Snakefile, which does a lot of post-alignment quality control (CollectInsertSizeMetics, CollectAlignmentSummaryMetrics, CollectGcBiasMetrics, ...). At the very end of the Snakefile, I am running multiQC to combine all the…
nhaus
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Snakemake - can you access job properties from within the jobscript?

The default snakemake jobscript looks like this: #!/bin/sh # properties = {properties} {exec_job} I have modified it a bit to print some useful information: #!/bin/sh # properties = {properties} hostname=`hostname` echo "Running on…
soungalo
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How to use the expand function in Snakemake to make permutations or combinations of a list

probably a very basic question in Snakemake but I couldn't find the answer so far. Say I have a list of samples SAMPLES = ["A", "B", "C"] A typical expand command would look like: expand("{sample}.txt", sample=SAMPLES) But I would like to get…
Lore Ament
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Snakemake, RNA-seq : How can I execute one subpart of a pipeline or another subpart based on the characteristics of the sample that is analysed?

I am using snakemake to design a RNAseq-data analysis pipeline. While I've managed to do that, I want to make my pipeline to be as adaptable as possible and make it able to deal with single-reads (SE) data or paired-end (PE) data within the same run…
athiebaut
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Snakemake : Can I access wildcards outside of rules?

Is it possible to access a snakemake wildcards outside of a rule ?
athiebaut
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Rule in snakemake using singularity: unterminated quoted string

I'm running a snakemake pipeline that for a specific rule loads a container: rule counts: params: transcriptome=os.environ["INDEX"], outdir= (os.environ["OUTDIR"] + "/counts/"), indir= (os.environ["INDIR"] + "{sample}"), name =…
compuTE
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Snakemake multiple Config Files?

Quick question regarding snakemake and using more than one config file. I'm creating a rather large pipeline for genomic preProcessing, and the idea is that it is user-friendly and accounts for the lowest-common-denominator in terms of user…
epigenome
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Conditional execution of one rule or another depending on the arguments given to a snakemake pipeline

I am creating a snakemake pipeline where I have, in some point, to filter my results. But there are two kind of filters that I could apply, so I would like to give it as an argument when launching the pipelin and then, depending on the argument, I…
Jeni
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What are the conditions for snakemake to execute a job?

I would like to know all necessary criteria required for snakemake to decide that a job needs to be executed, but I couldn't find them in their documentation. The best source I have found is in snakemake author's slides from 2016, which says: A job…
Manavalan Gajapathy
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Would it make sense to use Snakemake and Dask together?

I have a Snakemake workflow that I've been using to train DL TensorFlow models. At a high level there are a few longish-running jobs (model training) that can be run in parallel. I would like to run these on the cloud and dask-cloudprovider seems…
j sad
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How to use Singularity in docker container?

I have a question about the official Snakemake container image. https://hub.docker.com/r/snakemake/snakemake/dockerfile In this Dockerfile, singularity will be installed. As far as I know, the --privileged argument seems to be required to use…
tetsuro90
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