Published February 17, 2023 | Version v1.0.0
Software Open

The nf-core framework for community-curated bioinformatics pipelines.

Authors/Creators

Description

v1.0.0 - February 2023

Initial release of Arcadia-Science/seqqc, created with the nf-core template.

Added
  • Local module to download sourmash contamination database
  • Workflow to run sourmash gather to detect routine contamination
  • Workflow to run sourmash compare to determine sequence similarity between samples
  • Integration of sourmash outputs into the MultiQC outputs (when run with docker profile only)
  • Conda, Docker, and Singularity integration
  • Documentation for the pipeline
  • MultiQC interpretation documentation
  • Test profiles for different sequencing chemistries
  • Updates to email template
  • Added the cron job that automatically triggers the pipeline runs using GitHub actions, AWS S3, and AWS Batch via Nextflow Tower
Fixed Dependencies
  • fastqc=0.11.9
  • multiqc=1.14 # currently installed from a dev branch
  • sourmash=4.6.1
  • gnu-wget=1.18
Deprecated

Notes

If you use `nf-core tools` in your work, please cite the `nf-core` publication

Files

Arcadia-Science/seqqc-v1.0.0.zip

Files (2.2 MB)

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Additional details

Related works

Is supplement to
https://github.com/Arcadia-Science/seqqc/tree/v1.0.0 (URL)