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Modular Nextflow Pipeline for SRR → Assembly → Amplicons → Pairwise Matrix

This repository provides a modular, Singularity-based Nextflow (DSL2) pipeline for:

  1. Downloading raw reads from NCBI SRA (SRR accessions)
  2. Assembling reads with Shovill
  3. Predicting in‑silico amplicons using EMBOSS primersearch
  4. Generating a pairwise difference matrix from amplicon FASTA files

Pipeline stages and data flow

SRR list
   │
   ▼
fastqs/          (download)
   │
   ▼
assemblies/      (shovill)
   │
   ▼
amplicons/       (primersearch)
   │
   ▼
pairwise matrix  (CSV)

Directory structure

When all stages are run, outputs are written under a single --outdir.

results/
├── fastqs/
│   ├── SRR123_1.fastq.gz
│   ├── SRR123_2.fastq.gz
│   └── ...
├── assemblies/
│   │   └── SRR123_assembled.fasta
│   └── ...
├── primersearch/
│   ├── amplicon/
│   │   ├── SRR123_assembled_extractedAmplicons.fasta
│   │   ├── SRR123_assembled_not_matched_primers.txt
│   ├── SRR123_assembled.fasta
│   ├── SRR123.json
│   ├── SRR123.ps
│   └── ...
├── matrix_rows/
│   │   └── SRR123_assembled_extractedAmplicons.txt
│   └── ...
└── matrix/
    └── pairwise_diff_matrix.csv

Common usage patterns

1. Full pipeline: SRR → matrix

nextflow run main.nf \
   --srr_list <SRR list file (one SRR per row)> \
   --outdir $PWD/<output folder> (need to use absolute path, or prefix it with $PWD\
   --primers <primer file (3-column primersearch format)> \ 
    --output_csv pairwise_test_50srrs.csv

2. Download-only (raw FASTQ files from SRA)

nextflow run main.nf -entry download_only \
    --srr_list srr_ids.txt \
    --outdir results

3. Assembly-only (skip SRA download)

nextflow run main.nf -entry assembly_only \
    --reads /path/to/fastqs \
    --outdir results

4. Download + assembly (da)

nextflow run main.nf -entry da \
    --srr_list srr_ids.txt \
    --outdir results

5. Primersearch-only

nextflow run main.nf -entry primersearch_only \
    --reads /path/to/assemblies \
    --primers primers.txt \
    --outdir results \

6. Pairwise-only

nextflow run main.nf -entry pairwise_only \
    --amplicon_folder $PWD/amplicons (need to use absolute path, or prefix it with $PWD \
    --primers primers.txt \
    --output_csv pairwise.csv \
    --outdir output_folder

7. Primersearch + pairwise matrix (pp)

nextflow run main.nf -entry pp \
    --reads assemblies \
    --primers primers.txt \
    --outdir $PWD/results  (need to use absolute path, or prefix it with $PWD\
    --output_csv pairwise.csv

Repository layout

.
├── main.nf
├── nextflow.config
├── modules/
│   ├── download_reads.nf
│   ├── assemble_shovill.nf
│   ├── primersearch_amplicons.nf
│   └── pairwise_matrix.nf
├── bin/
│   ├── parse_primersearch.py
│   ├── fasta_to_json.py
│   ├── pairwise_compare.py
│   └── merge_rows.py
└── README.md

Notices

Public Domain Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

Privacy Notice

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Contributing Notice

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records Management Notice

This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.