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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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Missing input files from a directory with Snakemake

I'm trying to write a script for a pipeline, but I'm having trouble declaring the input of a rule from a directory. My code in these parts: rule taco: input: all_gtf = GTF_DIR + "path_samplesGTF.txt" output: taco_out…
Leandro Boralli
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Bare bones necessary to run pipeline on snakemake?

I have to perform imputation of genetic information, but scripts and files are located on different locations. There are some parallel jobs for could (cluster) involved as well. Too much of a manual running-waiting is necessary to get job done. In…
juststuck
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How to target HDF5 datasets as Snakemake input/output?

How can I tell Snakemake that the input/output of a rule should be an HDF5 dataset (so with its own specific "path" within the actual real HDF5 file path)?
Nisba
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Snakemake read input from file

I am trying to use file that will be written during the run as an input to another rule, but it always give me error FileNotFoundError: [Errno 2] No such file or directory: Is there a way to fix it or other implementation to have the same logic. def…
Medhat
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How can I run a subset of my snakemake rules several times with wildcards?

I have a snakemake pipeline in which the input files are divided into two groups - input I would like to pass through the entire pipeline (true input) and input that should only pass through the first few rules (control input). How can I pass the…
Tobi
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Can a snakemake rule allow empty output files?

I have a rule in a snakemake workflow that might produce an empty output file, depending on the input. That output file is then used in another rule whose command will be totally ok with an empty file as input, as long as the path exists for that…
Colin
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Run entire Snakemake pipeline in a scratch space

I'm wondering if it's possible to run the entire Snakemake pipeline in a scratch space? I understand that the shadow directive allows one to run rules in isolated directories, but is it possible to do that for entire pipeline without having to write…
Vivek Rai
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split bam files to (variable) pre-defined number of small bam files depending on the sample

I want to split multiple bam files to pre-determined number of smaller bam files. I do not know how to specify the output because the number of smaller bam files is variable depending on which samples I am splitting. I have read…
crazyhottommy
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How to access variables defined in the snakefile in a snakemake wrapper?

I would like to write a snakemake wrapper able to adapt its behaviour based on the value of variables defined in the main snakefile. This doesn't seem to simply work, I get a NameError when I try to use such a variable in the wrapper. In particular,…
bli
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How to ensure snakemake rule dependency while submitting via qsub

I am using Snakemake to submit jobs to the cluster. I am facing a situation where I would like to force a particular rule to run only after all other rules have run - this is because the input files for this job (R script) are not yet ready. I…
user10101904
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Snakemake on gatk VariantRecalibrator

I am new in using snakemake, I have an issue when doing the step gatk VariantRecalibrator on snakemake, it generated error but the script can run without error when not in snakemake format. import snakemake.io import…
Peter Chung
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Snakemake - input function exception

I am trying to run snakemake code using.json file as input. While checking the dry run i got foloowing error InputFunctionException in line 172 of /home/Snakefile_ChIPseq_pe: KeyError: '130241_1' Wildcards: library=130241_1 This is the part of…
RonicK
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Snakemake › Access multiple keys from config file

I have the question about the proper handling of the config file. I'm trying to solve my issue for a couple of days now but with the best will, I just can't find out how to do it. I know that this question is maybe quite similar with all the others…
VcFbnne
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Why one snakemake rule is always skipped or ignored

I am trying to fix a Snakefile. There are two rules (see the code below), each one would work if it's the only one, but only the rule prernaseqc would work when both are kept. It seems that snakemake totally ignores the other. I tried to touch file…
coder2019
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Snakemake report error:Missing input files for rulle all

I'm writing my RNA-seq pipeline using Snakemake. When I was writing the last part rule fpkm, which calculates fpkm value from bam files, I get the error: MissingInputException in line 3 of /root/s/r/snakemake/my_rnaseq_data/Snakefile: Missing input…
shebentao
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