Questions tagged [snakemake]

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4
votes
2answers
57 views

How do I write tests for a snakemake pipeline?

I've been playing with snakemake, which is really powerful, however, I'd like to create a 'unit test' for the whole pipeline. e.g. a way to call the pipeline that tests that all the rules work ...
1
vote
1answer
68 views

using snakemake shadow rules to store temp files on local nodes

Snakemake is not really designed to store temporary files to local disk, but in the documentation, they suggest a workaround using "shadow rules". The problem I have is, that our front node ...
0
votes
1answer
31 views

Removing data from OrthoFinder output prefix

I am using OrthoFinder to find orthogroups between species. I am using the latest version unpacked through tar as per their instructions. Orthofinder creates an output folder according to the current ...
0
votes
1answer
40 views

snakemake - using output file not explicitly declared as input for subsequent rule

I am writing a snakemake that, up to now should use raw sequencing reads to produce a draft assembly using canu use minimap2 to align the raw reads against the draft assembly, generated by canu. ...
1
vote
1answer
44 views

EGA remote download via snakemake fails due to EGA_CLIENT_ID specification

The example code provided by the Snakemake documentation for remote downloading from the EGA archive fails for me. I have defined all required environment variables, but an error comes up stating <...
6
votes
2answers
72 views

How to modify execution orders for Snakemake?

My goal is to process two samples, S1 and S2, using two rules, step1, ...
1
vote
2answers
195 views

Can't install snakemake v5.15.0 from conda

I'm trying to install the latest version of snakemake from conda into a conda env, following the instructions here. I.e. ...
1
vote
2answers
82 views

Running snakemake with multiple conda environments without rebuilding environments every time

I have some snakemake pipelines that have rules which run in different environments. Is it possible to run the pipeline without having to rebuild the environments from scratch every time when run in a ...
0
votes
1answer
18 views

How to run a one-time 'setup' step for amrfinder in snakemake using conda

I'm trying to add amrfinder running within conda to a snakemake workflow, working on a slurm HPC. The first time you run amrfinder, you have to run ...
2
votes
1answer
34 views

How to concatename file names in Snakemake?

I want to pass a series of files (e.g., a, b) to a program prog like: ...
2
votes
1answer
78 views

conda doesn't install latest version of snakemake

I would like to use the --default-resources parameter for profiles which is available in later versions of snakemake. To install snakemake, I created a new conda ...
1
vote
1answer
69 views

Snakemake on cluster produces empty output files

Problem: When I run my Snakefile on our cluster, all the processes complete successfully. I can see from the logs that my shell scripts are being run correctly and are claiming to complete ...
3
votes
1answer
56 views

truncate fastq.gz file without error in Snakemake

All, As the first step in my Snakemake pipeline, I generate small fastq files from all input fastq.gz files. This is to run a quick round of "infer_experiment.py" (from RSeQC, to get the kit ...
0
votes
2answers
64 views

Prevent Snakemake from changing wildcards: sample for every rule

EDIT: I posted this as a bug, perhaps wait for the result of that? github All, I am using Snakemake to build a pipeline. To define input and output names, I constructed them based on a filename base ...
4
votes
1answer
140 views

Snakemake: Migrating from deprecated cluster.json to new profiles.yaml

I am an avid user of Snakemake. Recently we have been refreshing our pipelines and I saw that a cluster.json file is no longer the recommended way to store the cluster configuration. I used to start ...
2
votes
0answers
43 views

NA12878 equivalent for somatic variant calling [duplicate]

I'm building a somatic variant calling pipeline with snakemake. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. ...
0
votes
0answers
119 views

“IndexError: list index out of range” in snakemake

I am trying to establish pipeline in snakePipes and while running DNA mapping I got next IndexError error. ...
2
votes
1answer
621 views

snakemake with --conda-prefix, can I use a pre-built conda environment?

I have read this question (Running Snakemake in one single conda env) but still have some doubt. I am using the '--conda-prefix /some/dir' option and I have a rule in my snakemake file with the ...
1
vote
1answer
292 views

snakemake get environment variable for rule name and log path

When a rule fails in snakemake workflow, it returns a descriptive message in log file like following: ...
3
votes
1answer
104 views

Access workdir defined on command line from within Snakefile

Snakemake provides access to a workflow object within a Snakefile. This allows one to, for example, have dynamic programmatic access to the directory containing the ...
5
votes
1answer
232 views

How can I ask snakemake to produce a dag where each node represents a rule?

I am using snakemake to create workflows. It is very convenient to visualise my DAG using ...
1
vote
1answer
84 views

How can I specify an email address in the SLURM snakemake json configuration file?

I am working on a SLURM-based cluster. I am currently using the following slurm json file: ...
1
vote
1answer
2k views

Mix globbing and wildcards when specifying rule input

Consider the following scenario. ...
2
votes
1answer
103 views

Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?

I searched for the package 'snakemake' on my SLURM cluster using: conda search --channel bioconda snakemake and I get many versions, up to 5.4.2. I then try to ...
9
votes
3answers
2k views

Running Snakemake in one single conda env

I have been experimenting a lot lately with Snakemake, I love it. Recently I also switched to using conda (--use-conda) in the way that is advertised. However, I have some issues with it, mostly ...
2
votes
1answer
406 views

Python string editing in Snakemake

I'm running a custom perl script using Snakemake. I use this rule: ...
3
votes
2answers
2k views

'Wildcards' object has no attribute 'sample'

I'm using Snakemake and I'm trying to get all my QC reports into multiqc but I get the following error: ...
2
votes
1answer
758 views

Snakemake: Cannot find first rule?

Back again with another snakemake query. This time I decided to port my read cleaning and alignment pipeline to snakemake. Repeating the steps from previous question and trying not to make any typo ...
1
vote
1answer
98 views

Snakemake and SLURM -unable to use it with with --cluster

I'm trying to automate some of my previous bash scripts with snakemake. Below is one of the recipe I created: ...
1
vote
1answer
853 views

Output file names are not known beforehand

I have a folder where the hdf5 files inputs are (matrices of scRNAseq raw UMI counts). There ...
8
votes
2answers
3k views

Running SnakeMake on cluster

I do not understand how to specify correctly the parameters on a SLURM cluster for snakemake to use them. I tried submitting the ...
4
votes
3answers
1k views

How to specify resources for cluster in snakemake

I am trying to run snakemake version 3.5.4 on my cluster, where jobs are partially defined by a common template build according ...
7
votes
2answers
4k views

How to resolve in snakemake error : “Target rules may not contain wildcards.”

I would like to do easily reproducible analysis using publicly available data from NCBI, so I have chosen a snakemake. I would like to write a single rule, that ...
1
vote
1answer
1k views

snakemake rule all

I am trying snakemake for my mRNA-seq pipeline and I got stuck in a simple thing. ...
5
votes
1answer
133 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
6
votes
2answers
427 views

combining the use of workdir and option --jobscript in snakemake

It seems that in snakemake the script specified after the --jobscript cannot be used properly if a workdir: is specified in the ...
7
votes
2answers
729 views

How are snakemake's --cluster and --drmaa options implemented?

I'm fairly new to snakemake and I'm trying to understand the difference between the --cluster and --drmaa flags, both of which ...