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sanger-tol / ascc

A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.
https://pipelines.tol.sanger.ac.uk/ascc
MIT License
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genomics nextflow pipeline

readme

Cite with Zenodo

Nextflow run with conda run with docker run with singularity Launch on Nextflow Tower

THIS IS AN IN-DEVELOPMENT PIPELINE THAT IS CURRENTLY NOT READY FOR ANY USE

AS SUCH YOU MAY FIND THAT THE DOCUMENTATION DOES NOT MATCH THE CODE AND IT MAY NOT WORK

ONCE THE PIPELINE REACHES A USABLE STATE A TAGGED RELEASE/PRE-RELEASE WILL BE MADE

Introduction

sanger-tol/ascc is a bioinformatics pipeline that ...

  1. Read QC (FastQC)
  2. Present QC for raw reads (MultiQC)

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run sanger-tol/ascc \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/ascc was originally written by eeaunin.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.