nf-ducken

Workflow to process amplicon meta-analysis data, from either local FASTQs or NCBI accession IDs to taxonomic classification.

Environment

Conda

Note for users with newer Apple processors (M1/M2): Conda environments require emulation using Rosetta, due to the lack of certain packages for the ARM64 architecture otherwise available with Intel processors. Please follow the installation and setup instructions here for details.

Conda environments are available for all processes. Launch a Conda environment-based run using -profile conda when running the workflow script.

Singularity and Docker

Containers are available for all processes. Launch a container-based run with Singularity or Docker using -profile docker or -profile singularity when running the workflow script.

Outputs

• outDir/taxonomy.qza: Artifact containing frequencies for features collapsed to a given level (default genus).
• outDir/taxonomy.qzv: Visualization containing frequencies for features collapsed to a given level (default genus).
• outDir/feature_table.qza: Artifact containing table of represented features by sample.
• outDir/stats/: Directory containing QC metrics, including FastQC, clustering statistics, denoising statistics, etc.
• outDir/trace/: Directory containing runtime metrics with an execution report and a pipeline DAG.

Process

Steps

1. Data import (qiime tools import) or FASTQ download (q2-fondue)
2. Optional adapter trimming: q2-cutadapt
3. Initial quality control and denoising: q2-dada2
4. Optional chimera filtering: q2-vsearch
5. Closed reference OTU clustering: q2-vsearch
6. Taxonomy classification: q2-feature-classifier
7. Collapse to taxon of interest and merge final outputs

Execution

nextflow run /path/to/workflow/main.nf -c run.config -profile conda

By default, workflow inputs may be entered as TSV or FASTQ files; the workflow is designed to generate input QIIME 2 artifacts using the import/download processes. This behavior is controlled by the generate_input parameter, set to true by default.

To use an already-created input QIIME 2 artifact, the user should set params.generate_input to false and specify the path to the input artifact using the params.input_artifact parameter. For example:

--generate_input false --input_artifact "path/to/input_artifact"