https://github.com/tiagofilipe12/patlasflow
A pipeline to run mapping, mash screen and assembly methods for pATLAS.
https://github.com/tiagofilipe12/patlasflow
bowtie2 mash nextflow patlas pipeline samtools
Last synced: 2 months ago
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A pipeline to run mapping, mash screen and assembly methods for pATLAS.
- Host: GitHub
- URL: https://github.com/tiagofilipe12/patlasflow
- Owner: tiagofilipe12
- License: gpl-3.0
- Created: 2018-01-30T13:59:20.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-01-04T11:49:29.000Z (over 6 years ago)
- Last Synced: 2025-02-13T02:32:49.677Z (4 months ago)
- Topics: bowtie2, mash, nextflow, patlas, pipeline, samtools
- Language: Python
- Homepage:
- Size: 87.9 KB
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pATLASflow
[](#)
[](https://hub.docker.com/r/tiagofilipe12/patlasflow_mash_screen/)
[](https://hub.docker.com/r/tiagofilipe12/patlasflow_mapping/)
[](https://github.com/tiagofilipe12/pATLAS)
A pipeline to run mapping, mash screen and assembly methods for pATLAS.
# TOC
* [Brief description](#brief-description)
* [Requirements](#requirements)
* [Conda recipe for nextflow](#conda-recipe-for-nextflow)
* [Usage](#usage)
* [Example run](#example-run)
* [TL;DR](#tldr)
## TL;DR
1. Read files must be placed in `/reads/` folder
2. Fasta files must be placed in `/fasta/` folder
3. Run the pipeline `nextflow run tiagofilipe12/pATLASflow` with the options you require:
* Assembly: `nextflow run tiagofilipe12/pATLASflow --assembly`
* Mapping: `nextflow run tiagofilipe12/pATLASflow --mapping`
* Mash screen: `nextflow run tiagofilipe12/pATLASflow --mash_screen`
Note: you can even run all approaches by doing:
`nextflow run tiagofilipe12/pATLASflow --assembly --mapping --mash_screen`
## Brief description
This Nextflow script is an implementation of [mash-wrapper](https://github.com/tiagofilipe12/mash_wrapper#mash-screen-for-read-samples)
for mash screen module.
It will output a `JSON` file that can be imported into [pATLAS](http://www.patlas.site).
## Requirements
First of all, pATLASflow is a Nextflow pipeline and thus does not
require the installation of third party programs since they are provided
through docker container that can be used both with singularity and
docker.
* [Java 8](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or higher.
* [Docker](https://docs.docker.com/install/) or [Singularity](http://singularity.lbl.gov/install-linux).
* [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) - follow the two installation steps (there is no need to read anything else).
### Conda recipe for nextflow
If you prefer you can use this conda recipe for nextflow: [](http://bioconda.github.io/recipes/nextflow/README.html)
```
conda install nextflow
```
## Usage
```
Usage: nextflow run tiagofilipe12/pATLASflow [options] or nextflow run main.nf [options] or ./main.nf [options]
Nextflow magic options:
-profile Forces nextflow to run with docker or singularity. Default: standard Choices: standard, singularity, slurm
Main options:
--help Opens this help. It will open only when --help is provided. So, yes, this line is pretty useless since you already know that if you reached here.
--version Prints the version of the pipeline script.
--mash_screen Enables mash screen run.
--assembly Enables mash dist run to use fasta file against plasmid db
--mapping Enables mapping pipeline.
Mash options:
--kMer the length of the kmer to be used by mash. Default: 21
--pValue The p-value cutoff. Default: 0.05
Mash screen exclusive options:
--identity The minimum identity value between two sequences. Default: 0.9
--noWinner This option allows to disable the -w option of mash screen Default: false
Mash dist exclusive options:
--mash_distance Provide the maximum distance between two plasmids to be reported. Default: 0.1
Reads options:
--reads The path to the read files. Here users may provide many samples in the same directory. However be assured that glob pattern is unique (e.g. 'path/to/*_{1,2}.fastq').
--singleEnd Provide this option if you have single-end reads. By default the pipeline will assume that you provide paired-end reads. Default: false
Fasta options:
--fasta Provide fasta file pattern to be searched by nextflow. Default: 'fasta/*.fas'
Bowtie2 options:
--trim5 Provide parameter -5 to bowtie2 allowing to trim 5' end. Default: 0
--cov_cutoff Provide a cutoff value to filter results for coverage results. Default: 0.60
```
## Example run
`nextflow run tiagofilipe12/pATLASflow --assembly`
## Slurm profile
One can run this pipeline using the `slurm` profile, which enalbes to
use it with `shifter` and slurm.
### IMM-lobo users
In order to avoid the usage of `compute-1` you need to uncomment line
[62 in nextflow.config](https://github.com/tiagofilipe12/pATLASflow/blob/master/nextflow.config#L62) file.
## Results
Results will be placed in a folder named `results` within the current working
directory.