Snakemake is a workflow management system with a Python-style specification language.
Snakemake is a workflow management system with a Python-style specification language.
Questions tagged [snakemake]
1634 questions
4
votes
1 answer
Parallelizing snakemake rule
Sorry if this is a naive question, but I'm still trying to wrap my head around the intricacies of Snakemake.
I have a directory containing a number of files that I want to apply a rule to in parallel (i.e. I want to submit the same script to the…
bdevil
- 185
- 1
- 12
4
votes
2 answers
Snakemake: Avoid removing output files before executing the shell command
Is there a possibility to avoid that the output files defined in a snakemake rule are deleted before executing the shell command? I found a description of this behaviour here:…
SarahH
- 43
- 4
4
votes
1 answer
How to set threads based on number of cores available?
I have a workflow that runs on different machines with different numbers of CPUs, and I'd like to be able to setup a rule that uses "all but N" cores. I.e. I'd like to be able to do:
threads: lambda cores: max(2, cores-4)
But I cannot find any way…
tfenne
- 63
- 3
4
votes
1 answer
Snakemake one wildcard and also expand
Is it possible to have a snakemake with a wildcard and expand:
rule a:
input:
"input/{first}.txt",
expand("data/{second}.txt", second=A_LIST)
output:
expand("output/{first}_{second}, second=A_LIST)
Parsa
- 3,054
- 3
- 19
- 35
4
votes
2 answers
How to keep the snakemake shell file while running in cluster
While running my snakemake file in cluster I keep getting an error,
snakemake -j 20 --cluster "qsub -o out.txt -e err.txt -q debug" -s
seadragon/scripts/viral_hisat.snake --config json=""
output="
Hirak Sarkar
- 125
- 8
4
votes
3 answers
Snakemake: How do I use a function that takes in a wildcard and returns a value?
I have cram(bam) files that I want to split by read group. This requires reading the header and extracting the read group ids.
I have this function which does that in my Snakemake file:
def identify_read_groups(cram_file):
import subprocess
…
David M
- 149
- 1
- 9
4
votes
5 answers
How to perform simple string operations in snakemake output
I am creating my first snakemake file, and I got to the point where I need to perform a simple string operation on the value of my output, so that my shell command works as expected:
rule sketch:
input:
'out/genomes.txt'
output:
…
mgalardini
- 1,397
- 2
- 16
- 30
4
votes
1 answer
Use of argparse in Snakemake script
Is it possible to pass custom command line arguments to snakemake scripts? I have tried, but executing Snakefile with argparse results in error snakemake: error: unrecognized arguments: -zz. Below is an example script.
import argparse
def…
Manavalan Gajapathy
- 3,900
- 2
- 20
- 43
4
votes
2 answers
snakemake wildcards or expand command
I want a rule to perform realignment between normal and tumor. The main problem is I don't know how to manage that problem. Is it the wildcard or the expand the answer to my problem?
This is my list of samples:
conditions:
pair1:
tumor:…
mau_who
- 315
- 2
- 13
4
votes
1 answer
Thread.py error snakemake
I am trying to run a simple one-rule snakemake file as following:
resources_dir='resources'
rule downloadReference:
output:
fa = resources_dir+'/human_g1k_v37.fasta',
fai = resources_dir+'/human_g1k_v37.fasta.fai',
shell:
…
Masih
- 920
- 2
- 19
- 36
4
votes
1 answer
MissinOutputException in snakemake
I'm planning to move my bioinformatics pipeline into snakemake as my current pipeline is a collection of multiple scripts that are increasingly hard to follow. On the basis of tutorials and documentation, snakemake seems to be very clear and…
Jokhe
- 77
- 1
- 7
4
votes
1 answer
Using pyenv in a snakemake rule
I am using snakemake for a long and complicated pipeline which involves some externally written python2 scripts. When I try to specify python2 with pyenv, pyenv shell command fails while pyenv global and pyenv local have no effect. I have two…
rbrisk
- 306
- 1
- 7
4
votes
1 answer
Subprocess: Can't convert '_io.BufferedReader' object to str implicitly
I am working on writing a script which is a combination of snakemake and python code to automate a large number of files that comes in pair. More precisely, I am working on aligning reads with BWA MEM with paired end reads…
Zen
- 41
- 1
- 5
4
votes
1 answer
Snakemake best practice for demultiplexing
I have a question about best practices. Specifically, about the best snakemake pattern for demultiplexing reads from illumina sequencing. Our workflow needs to demultiplex multiple lanes of sequencing, and then combine these in a single analysis.…
kdmurrray91
- 365
- 1
- 8
4
votes
4 answers
snakemake: is there a way to specify an output directory for each rule?
The scripts I used all put the output files to the current directory where the script was called so in my shell script pipeline I would have cd commands to go to a particular directory to run commands and output files will just be saved in relevant…
olala
- 4,146
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