nf-core-aMeta: A Nextflow repository from ZoePochon

Introduction

nf-core/ameta is a bioinformatics pipeline that is a conversion of the ancient microbiome analysis workflow written in Snakemake: https://github.com/NBISweden/aMeta.

Read QC (FastQC)
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.

Important

Prebuilt databases are available from:

KrakenUniq DB on full NCBI NT: https://doi.org/10.17044/scilifelab.20205504
KrakenUniq DB on microbial part of NCBI NT: https://doi.org/10.17044/scilifelab.20518251
KrakenUniq DB on microbial part of NCBI RefSeq: https://doi.org/10.17044/scilifelab.21299541
Bowtie2 index for full NCBI NT database: https://doi.org/10.17044/scilifelab.21070063
Bowtie2 index on pathogenic microbes of NCBI NT: https://doi.org/10.17044/scilifelab.21185887

Now, you can run the pipeline using:

nextflow run nf-core/ameta \
   -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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/ameta was originally written by @mahesh-panchal.

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.

For further information or help, don't hesitate to get in touch on the Slack #ameta channel (you can join with this invite).

Citations

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

You can cite the nf-core publication as follows: