Routine Assembly

A generic pipeline for creating routine draft assemblies

Analyses

• Read trimming & QC: fastp
• Genome Assembly: shovill or unicycler
• Gene Annotation: prokka or bakta
• Assembly QC: quast

Usage

By default, shovill and prokka will be used:

nextflow run BCCDC-PHL/routine-assembly-nf \
  --fastq_input <fastq input directory> \
  --outdir <output directory>

Unicycler and/or bakta can be used with the --unicycler and --bakta flags:

nextflow run BCCDC-PHL/routine-assembly-nf \
  --fastq_input <fastq input directory> \
  --unicycler \
  --bakta \
  --outdir <output directory>

Any combination of shovill/unicycler and prokka/bakta is supported: Shovill with bakta:

nextflow run BCCDC-PHL/routine-assembly-nf \
  --fastq_input <fastq input directory> \
  --bakta \
  --outdir <output directory>

Unicycler with prokka:

nextflow run BCCDC-PHL/routine-assembly-nf \
  --fastq_input <fastq input directory> \
  --unicycler \
  --outdir <output directory>

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

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

Output

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).

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

sample-01
├── sample-01_20211125165316_provenance.yml
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_shovill_prokka.gbk
├── sample-01_shovill_prokka.gff
├── sample-01_shovill_quast.csv
├── sample-01_shovill.fa
└── sample-01_shovill.log

Including the tool name suffixes to output files allows re-analysis of the same sample with multiple tools without conflicting output filenames:

sample-01
├── sample-01_20211125165316_provenance.yml
├── sample-01_20211128122118_provenance.yml
├── sample-01_unicycler_bakta.gbk
├── sample-01_unicycler_bakta.gff
├── sample-01_unicycler_bakta.json
├── sample-01_unicycler_bakta.log
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_shovill_prokka.gbk
├── sample-01_shovill_prokka.gff
├── sample-01_shovill_quast.csv
├── sample-01_unicycler_quast.csv
├── sample-01_shovill.fa
├── sample-01_shovill.log
├── sample-01_unicycler.fa
├── sample-01_unicycler.gfa
└── sample-01_unicycler.log

Provenance files

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

- tool_name: fastp
  tool_version: 0.23.1
- tool_name: shovill
  tool_version: 1.1.0
- tool_name: prokka
  tool_version: 1.14.5
- tool_name: quast
  tool_version: 5.0.2
- input_filename: sample-01_R1.fastq.gz
  sha256: 4ac3055ac5f03114a005aff033e7018ea98486cbebdae669880e3f0511ed21bb
- input_filename: sample-01_R2.fastq.gz
  sha256: 8db388f56a51920752319c67b5308c7e99f2a566ca83311037a425f8d6bb1ecc
- pipeline_name: BCCDC-PHL/routine-assembly
  pipeline_version: 0.1.0
- timestamp_analysis_start: 2021-11-25T16:53:10.549863

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.