Snakemake workflow: read-alignment-pangenome

A Snakemake workflow for aligning sequencing reads, including pangenome-graph alignment with vg giraffe, and producing final BAM + BAI per sample.

• Snakemake workflow: read-alignment-pangenome
  • Usage
  • Deployment options
  • Workflow profiles
  • Authors
  • References
  • TODO

Usage

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

Detailed information about input data and workflow configuration can also be found in config/README.md.

Main target and outputs

The main alignment target is:

• only_alignment

Expected final outputs (per sample):

• <results>/recal/{sample}.bam
• <results>/recal/{sample}.bai

The workflow currently produces final recalibrated BAM + BAI files per sample.

Note: If adapters is empty/NA in units.tsv, trimming with fastp is bypassed and raw reads are used.

Deployment options

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

cd path/to/read-alignment-pangenome

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

snakemake -n --cores 1 --use-conda only_alignment

To run the workflow with conda:

snakemake --cores 2 --use-conda only_alignment

To run the workflow with apptainer / singularity (optional), if containers are configured (e.g., via a workflow profile and/or rule-level container: directives):

snakemake --cores 2 --use-conda --use-apptainer only_alignment

Workflow profiles

The profiles/ directory can contain any number of workflow-specific profiles that users can choose from. The profiles README.md provides more details.

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

• Update the deployment, authors and references sections.
• Update the README.md badges. Add or remove badges for conda/singularity/apptainer usage depending on the workflow's deployment options.