diff --git a/README.md b/README.md index 1aef529..36976ae 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,9 @@ [![](https://img.shields.io/badge/nextflow->=0.27.3-blue.svg)](#) [![](https://img.shields.io/badge/docker_mash-ready-green.svg)](https://hub.docker.com/r/tiagofilipe12/patlasflow_mash_screen/) [![](https://img.shields.io/badge/docker_mapping-ready-green.svg)](https://hub.docker.com/r/tiagofilipe12/patlasflow_mapping/) +[![](https://img.shields.io/badge/pATLAS-1.x.x-lightgrey.svg)](https://github.com/tiagofilipe12/pATLAS) -A pipeline to run mash screen for pATLAS. +A pipeline to run mapping, mash screen and assembly methods for pATLAS. # TOC @@ -15,6 +16,21 @@ A pipeline to run mash screen for pATLAS. * [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) @@ -71,16 +87,3 @@ Usage: nextflow run tiagofilipe12/pATLASflow [options] or nextflow run main.nf [ `nextflow run tiagofilipe12/pATLASflow --assembly` -## 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`