A generic pipeline for creating long-read assemblies. Supports both long (Oxford Nanopore) reads, or hybrid assemblies with both short and long reads. Optionally annotate genes. Collects quality info on both incoming and outgoing datasets.
- Read trimming & QC: fastp and filtlong
- Genome Assembly: dragonflye (long reads, or hybrid)
- Gene Annotation: prokka or bakta
- Assembly QC: quast, bandage
By default, dragonflye will be used for assembly of long reads, and no gene annotation will be run:
nextflow run BCCDC-PHL/dragonflye-nf \
--long_only \
--fastq_input_long <long-read fastq input directory> \
--outdir <output directory>
...or a hybrid assembly can be generated by supplying short reads:
nextflow run BCCDC-PHL/dragonflye-nf \
--hybrid \
--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/dragonflye-nf \
--long_only \
--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/routine-assembly-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
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_dragonflye_short.fa
├── sample-01_dragonflye_short.log
└── sample-01_dragonflye_short_quast.csv
Including the tool name suffixes on 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_fastp.csv
├── sample-01_fastp.json
├── sample-01_dragonflye_hybrid_bakta.gbk
├── sample-01_dragonflye_hybrid_bakta.gff
├── sample-01_dragonflye_hybrid_bakta.json
├── sample-01_dragonflye_hybrid_bakta.log
├── sample-01_dragonflye_hybrid_bandage.png
├── sample-01_dragonflye_hybrid_prokka.gbk
├── sample-01_dragonflye_hybrid_prokka.gff
├── sample-01_dragonflye_hybrid_quast.csv
├── sample-01_dragonflye_hybrid_quast.csv
├── sample-01_dragonflye_hybrid.fa
├── sample-01_dragonflye_hybrid.gfa
├── sample-01_dragonflye_hybrid.log
├── sample-01_dragonflye_short_bakta.gbk
├── sample-01_dragonflye_short_bakta.gff
├── sample-01_dragonflye_short_bakta.json
├── sample-01_dragonflye_short_bakta.log
├── sample-01_dragonflye_short_bandage.png
├── sample-01_dragonflye_short_prokka.gbk
├── sample-01_dragonflye_short_prokka.gff
├── sample-01_dragonflye_short_quast.csv
├── sample-01_dragonflye_short_quast.csv
├── sample-01_dragonflye_short.fa
├── sample-01_dragonflye_short.gfa
└── sample-01_dragonflye_short.log
If the --versioned_outdir flag is used, then a sub-directory will be created below each sample, named with the pipeline name and minor version:
sample-01
└── dragonflye-nf-v0.4-output
├── sample-01_20220216172238_provenance.yml
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_dragonflye_short.fa
├── sample-01_dragonflye_short.log
├── sample-01_dragonflye_short_prokka.gbk
├── sample-01_dragonflye_short_prokka.gff
└── sample-01_dragonflye_short_quast.csv
This is provided as a way of combining outputs of several different pipelines or re-analysis with future versions of this pipeline:
sample-01
└── dragonflye-nf-v0.4-output
│ ├── sample-01_20220216172238_provenance.yml
│ ├── sample-01_fastp.csv
│ ├── sample-01_fastp.json
│ ├── sample-01_dragonflye_short.fa
│ ├── sample-01_dragonflye_short.log
│ ├── sample-01_dragonflye_short_prokka.gbk
│ ├── sample-01_dragonflye_short_prokka.gff
│ └── sample-01_dragonflye_short_quast.csv
└── dragonflye-nf-v0.5-output
├── sample-01_20220612091224_provenance.yml
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_dragonflye_short.fa
├── sample-01_dragonflye_short.log
├── sample-01_dragonflye_short_prokka.gbk
├── sample-01_dragonflye_short_prokka.gff
└── sample-01_dragonflye_short_quast.csv
For each pipeline invocation, each sample will produce a provenance.yml file with the following contents:
- pipeline_name: BCCDC-PHL/dragonflye-nf
pipeline_version: 0.4.0
- 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: dragonflye
tools:
- tool_name: dragonflye
tool_version: 1.1.0
- 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: nullThe 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.