https://github.com/ccdmb/nanopore_assembly
https://github.com/ccdmb/nanopore_assembly
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/ccdmb/nanopore_assembly
- Owner: ccdmb
- Created: 2022-05-18T04:05:38.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2023-05-10T00:07:30.000Z (about 3 years ago)
- Last Synced: 2025-09-09T23:31:23.684Z (9 months ago)
- Language: Nextflow
- Size: 21.5 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Nanopore assembly pipeline
This is a draft nanopore assembly pipeline used by some groups at the CCDM.
More documentation to come.
## Examples
```bash
nextflow run ccdmb/nanopore_assembly -resume -latest --nanoporeReads "*.fastq.gz"
```
## Profiles
We have a few profiles available to customise how the pipeline will run.
- `nimbus` sets the canu assembler to use 8 CPUs and 30GB RAM.
- `zeus` sets the canu assembler to use 14 CPUs and 64GB RAM, and sets some cluster specific options to use the slurm based scheduler at Pawsey.
- `docker` and `docker_sudo` sets it to use docker containers, `docker_sudo` is identical except that docker is run as root (required for some installations of docker).
- `singularity` sets it to use singularity containers, these are automatically converted from docker containers.
```bash
# Using docker
nextflow run ccdmb/nanopore_assembly -profile docker -resume -latest --nanoporeReads "*.fastq.gz"
# Using docker, and also increasing CPUs for canu.
nextflow run ccdmb/nanopore_assembly -profile docker,nimbus -resume -latest --nanoporeReads "*.fastq.gz"
```
## Parameters
```
--nanoporeReads
Required
A glob of the fastq.gz files of the adapter and barcode trimmed reads.
The basename of the file needs to match the basename of the respective genome.
--canuSlow
Default: false
Disables canu fast mode.
--outdir
Default: `assembly`
The directory to store the results in.
```