plasmid-assembly

A pipeline for high-quality plasmid assemblies.

Optionally annotate genes. Collects quality info on both incoming and outgoing datasets.

flowchart TD
  short_reads --> fastp(fastp)
  fastp -- trimmed_short_reads --> plassembler(plassembler)
  long_reads --> filtlong(filtlong)
  filtlong -- filtered_long_reads --> plassembler
  plassembler --> assembly[assembly]
  assembly --> prokka(prokka*)
  assembly --> bakta(bakta*)
  assembly --> quast(quast)
  assembly --> bandage(bandage)
  prokka --> prokka_annotated_assembly
  bakta --> bakta_annotated_assembly
  quast --> assembly_qc
  bandage --> assembly_diagram

*Optional processes

Analyses

Read trimming & QC: fastp and filtlong
Genome Assembly: plassembler (long reads, or hybrid)
Gene Annotation: prokka or bakta
Assembly QC: quast, bandage

Usage

By default, plassembler will be used, and no gene annotation will be run:

nextflow run BCCDC-PHL/plasmid-assembly \
  --fastq_input <short-read fastq input directory> \
  --fastq_input_long <long-read fastq input directory> \
  --outdir <output directory>

Prokka and/or bakta can be used with the --prokka and --bakta flags:

nextflow run BCCDC-PHL/plasmid-assembly \
  --fastq_input <short-read fastq input directory> \
  --fastq_input_long <long-read fastq input directory> \
  --prokka \
  --bakta \
  --outdir <output directory>

The pipeline also supports a 'samplesheet input' mode. Pass a samplesheet.csv file with the headers ID, R1, R2,LONG:

nextflow run BCCDC-PHL/dragonflye-nf \
  --samplesheet_input <samplesheet.csv> \
  --outdir <output directory>

Eg:

ID,R1,R2,LONG
sample-01,/path/to/sample-01_R1.fastq.gz,/path/to/sample-01_R2.fastq.gz,/path/to/sample-01_RL.fastq.gz
sample-02,/path/to/sample-02_R1.fastq.gz,/path/to/sample-02_R2.fastq.gz,/path/to/sample-02_RL.fastq.gz
sample-03,/path/to/sample-03_R1.fastq.gz,/path/to/sample-03_R2.fastq.gz,/path/to/sample-03_RL.fastq.gz

Output

(Note: this section is currently incomplete. Will be updated as output files are finalized)

An output directory will be created for each sample under the directory provided with the --outdir flag. The directory will be named by sample ID, inferred from the fastq files (all characters before the first underscore in the fastq filenames), or the ID field of the samplesheet, if one is used.

If we have sample-01_R{1,2}.fastq.gz, in our --fastq_input directory, the output directory will be:

sample-01
├── sample-01_20211125165316_provenance.yml
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_plassembler_hybrid.fa

Provenance files

For each pipeline invocation, each sample will produce a provenance.yml file with the following contents:

- pipeline_name: BCCDC-PHL/plasmid-assembly
  pipeline_version: 0.1.0
- timestamp_analysis_start: 2022-08-16T13:22:11.553143
- input_filename: sample-01_R1.fastq.gz
  sha256: 4ac3055ac5f03114a005aff033e7018ea98486cbebdae669880e3f0511ed21bb
  file_type: fastq-input
- input_filename: sample-01_R2.fastq.gz
  sha256: 8db388f56a51920752319c67b5308c7e99f2a566ca83311037a425f8d6bb1ecc
  file_type: fastq-input
- process_name: fastp
  tools:
    - tool_name: fastp
      tool_version: 0.23.1
- process_name: plassembler
  tools:
    - tool_name: plassembler
      tool_version: 1.4.1
- process_name: prokka
  tools:
    - tool_name: prokka
      tool_version: 1.14.5
      parameters:
        - parameter: --compliant
          value: null
- process_name: quast
  tools:
    - tool_name: quast
      tool_version: 5.0.2
      parameters:
        - parameter: --space-efficient
          value: null
        - parameter: --fast
          value: null

The filename of the provenance file includes a timestamp with format YYYYMMDDHHMMSS to ensure that re-analysis of the same sample will create a unique provenance.yml file.