Snakemake workflow: <name>

A Snakemake workflow for <description>

• Snakemake workflow: <name>
  • Usage
  • Workflow overview
  • Running the workflow
    • Input data
    • Execution
    • Parameters
  • Authors
  • References
  • TODO

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.

Workflow overview

This workflow is a best-practice workflow for <detailed description>. The workflow is built using snakemake and consists of the following steps:

1. Parse sample sheet containing sample meta data (python)
2. Simulate short read sequencing data on the fly (dwgsim)
3. Check quality of input read data (FastQC)
4. Trim adapters from input data (cutadapt)
5. Collect statistics from tool output (MultiQC)

Running the workflow

Input data

This template workflow creates artificial sequencing data in *.fastq.gz format. It does not contain actual input data. The simulated input files are nevertheless created based on a mandatory table linked in the config.yml file (default: .test/samples.tsv). The sample sheet has the following layout:

sample	condition	replicate	read1	read2
sample1	wild_type	1	sample1.bwa.read1.fastq.gz	sample1.bwa.read2.fastq.gz
sample2	wild_type	2	sample2.bwa.read1.fastq.gz	sample2.bwa.read2.fastq.gz

Execution

To run the workflow from command line, change the working directory.

cd path/to/snakemake-workflow-name

Adjust options in the default config file config/config.yml. Before running the entire workflow, you can perform a dry run using:

snakemake --dry-run

To run the complete workflow with test files using conda, execute the following command. The definition of the number of compute cores is mandatory.

snakemake --cores 3 --sdm conda --directory .test

To run the workflow with singularity / apptainer, add a link to a container registry in the Snakefile, for example: container: "oras://ghcr.io/<user>/<repository>:<version>" for Github's container registry. Run the workflow with:

snakemake --cores 3 --sdm conda apptainer --directory .test

Parameters

This table lists all parameters that can be used to run the workflow.

parameter	type	details	default
samplesheet
path	str	path to samplesheet, mandatory	"config/samples.tsv"
get_genome
database	str	one of manual, ncbi	ncbi
assembly	str	RefSeq ID	GCF_000006785.2
fasta	str	optional path to fasta file	Null
gff	str	optional path to gff file	Null
gff_source_type	str	list of name/value pairs for GFF source	see config file
simulate_reads
read_length	num	length of target reads in bp	100
read_number	num	number of total reads to be simulated	100000
random_freq	num	frequency of random read sequences	0.01
cutadapt
threep_adapter	str	sequence of the 3' adapter	-a ATCGTAGATCGG
fivep_adapter	str	sequence of the 5' adapter	-A GATGGCGATAGG
default	str	additional options passed to cutadapt	[-q 10 , -m 25 , -M 100, --overlap=5]
multiqc
config	str	path to multiQC config	config/multiqc_config.yml

Authors

• Firstname Lastname
  • Affiliation
  • ORCID profile
  • home page

References

Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., & Nahnsen, S. Sustainable data analysis with Snakemake. F1000Research, 10:33, 10, 33, 2021. https://doi.org/10.12688/f1000research.29032.2.

TODO

• Replace <owner> and <repo> everywhere in the template (also under .github/workflows) with the correct <repo> name and owning user or organization.
• Replace <name> with the workflow name (can be the same as <repo>).
• Replace <description> with a description of what the workflow does.
• Update the workflow description, parameters, running options, authors and references in the README.md
• Update the README.md badges. Add or remove badges for conda/singularity/apptainer usage depending on the workflow's capability
• The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if <owner> and <repo> were correctly set.