snippy-variants

Perform read mapping and variant calling using snippy.

flowchart TD
  reads --> fastp
  fastp -- trimmed_reads --> snippy
  snippy --> qualimap_bamqc
  snippy --> count_variants

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Usage

nextflow run BCCDC-PHL/snippy-variants \
  --ref </path/to/ref.fa> \
  --fastq_input </path/to/fastqs> \
  --outdir </path/to/output_dir>

Parameters

Flag	Default Value	Description
mincov	10	Minimum number of reads covering a site to be considered.
minfrac	0	Minimum proportion of those reads which must differ from the reference.
basequal	13	Minimum quality a nucleotide needs to be used in variant calling.
mapqual	60	Minimum mapping quality to accept in variant calling.

Output

An output directory will be created for each sample under the directory provided for the --outdir flag.

The following files will be produced for each sample:

.
└── sample-01
    ├── sample-01_TIMESTAMP_provenance.yml
    ├── sample-01.aligned.fa
    ├── sample-01.bam 
    ├── sample-01.bam.bai
    ├── sample-01_bamqc
    ├── sample-01.bed
    ├── sample-01.consensus.fa
    ├── sample-01.consensus.subs.fa
    ├── sample-01.csv 
    ├── sample-01_fastp.csv
    ├── sample-01_fastp.json
    ├── sample-01.filt.vcf
    ├── sample-01.gff
    ├── sample-01.html
    ├── sample-01.log
    ├── sample-01.raw.vcf
    ├── sample-01.report.txt
    ├── sample-01.subs.vcf
    ├── sample-01.tab 
    ├── sample-01.txt
    ├── sample-01.vcf
    ├── sample-01.vcf.gz
    ├── sample-01.vcf.gz.csi
    └── reference

Provenance

In the output directory for each sample, a provenance file will be written with the following format:

- pipeline_name: BCCDC-PHL/snippy-nf
  pipeline_version: 0.1.1
  nextflow_session_id: 9b6520b6-2997-495c-9dd1-34c96c4525a2
  nextflow_run_name: special_faggin
  analysis_start_time: 2025-08-22T13:13:54.936433-07:00
- input_filename: sample01_S12_L001_R1_001.fastq.gz
  file_type: fastq-input
  sha256: 925211cd402243bb4a2276e3751cd12b4d9aeb06f7cc2e7c266a5503a273bea3
- input_filename: sample01_S12_L001_R2_001.fastq.gz
  file_type: fastq-input
  sha256: 29e8a004bae2b98f4b1dbb42b122490210c1afd719987e2ae53b1242d696f70f
- process_name: fastp
  tools:
    - tool_name: fastp
      tool_version: 0.20.1
- process_name: snippy
  tools:
    - tool_name: snippy
      tool_version: 4.6.0
      parameters:
        - parameter: --mincov
          value: 10
        - parameter: --basequal
          value: 13
        - parameter: --mapqual
          value: 60
        - parameter: --minfrac
          value: 0
        - parameter: --ref
          value: H37Rv_NC000962.3.fasta
        - parameter: --R1
          value: sample01_trimmed_R1.fastq.gz
        - parameter: --R2
          value: sample01_trimmed_R2.fastq.gz
- process_name: qualimap
  tools:
    - tool_name: qualimap
      tool_version: v.2.2.2-dev
      subcommand: bamqc
      parameters:
        - parameter: --bam
          value: sample01.bam