Questions tagged [snakemake]

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2
votes
1answer
30 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
41 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
44 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
40 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
60 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. ...
1
vote
1answer
317 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
209 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
76 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
160 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
66 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
1k views

Mix globbing and wildcards when specifying rule input

Consider the following scenario. ...
2
votes
1answer
72 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 ...
8
votes
3answers
1k 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
325 views

Python string editing in Snakemake

I'm running a custom perl script using Snakemake. I use this rule: ...
3
votes
2answers
1k 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
448 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
87 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
662 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
2k 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
3k 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
113 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
6
votes
2answers
386 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 ...
6
votes
2answers
662 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 ...