update README

hoelzer-lab · Mar 6, 2022 · 50547cb · 50547cb
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@@ -1,8 +1,9 @@
 # RIBAP
 Roary ILP Bacterial Annotation Pipeline
 
-![](https://img.shields.io/badge/nextflow-20.01.0-brightgreen)
+![](https://img.shields.io/badge/nextflow-21.04.0-brightgreen)
 ![](https://img.shields.io/badge/uses-docker-blue.svg)
+![](https://img.shields.io/badge/uses-singularity-orange.svg)
 ![](https://img.shields.io/badge/uses-conda-yellow.svg)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
 
@@ -19,33 +20,71 @@ A common task when you have a bunch of bacterial genomes in your hands is the ca
 similarity often underestimates the _true_ core gene set, in particular when diverse species are compared. RIBAP combines sequence homology information from [Roary](https://github.com/sanger-pathogens/Roary) with smart pairwise [ILP](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391664/) calculations to produce a more complete core gene set - even on genus level. First, RIBAP performs annotations with [Prokka](https://github.com/tseemann/prokka), calculates the core gene set using [Roary](https://github.com/sanger-pathogens/Roary) and pairwise [ILPs](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391664/), and finally visualizes the results in an interactive HTML table garnished with protein multiple sequence alignments and trees. RIBAP comes with Nextflow and Docker/Conda support for easy execution.      
 
 # How can I give it a try?
-Easy, you just need a working `nextflow` and `docker` or `conda` installation, see below! You have `nextflow` and `docker`? Give it a try:
+Easy, you just need a working `nextflow` and `docker` or `singularity` or `conda` installation, see below! You have `nextflow` and `docker`? Give it a try:
 ```bash
 nextflow pull hoelzer-lab/ribap
-nextflow run hoelzer-lab/ribap -r 0.6.0 --fasta "$HOME/.nextflow/assets/hoelzer-lab/ribap/data/*.fasta" -profile local,docker
+nextflow info hoelzer-lab/ribap
+# select a release version, e.g. 0.7.0
+nextflow run hoelzer-lab/ribap -r 0.7.0 --fasta "$HOME/.nextflow/assets/hoelzer-lab/ribap/data/*.fasta" -profile local,docker
 ```
 You have `nextflow` and `conda`? Okay:
 ```bash
-nextflow run hoelzer-lab/ribap -r 0.6.0 --fasta "$HOME/.nextflow/assets/hoelzer-lab/ribap/data/*.fasta" -profile local,conda
+nextflow run hoelzer-lab/ribap -r 0.7.0 --fasta "$HOME/.nextflow/assets/hoelzer-lab/ribap/data/*.fasta" -profile local,conda
 ```
-You need some of this dependencies? See below. 
+You need some of this dependencies? Check the end of this README! 
 
-## Installation
+# Execution examples
+
+```bash
+# Get or update the workflow:
+nextflow pull hoelzer-lab/ribap
+
+# Run a specific release, check whats available:
+nextflow info hoelzer-lab/ribap
+
+# Or get newest release version automatically:
+REVISION=$(nextflow info hoelzer-lab/ribap | sed 's/ [*]//' | sed 's/ //g' | sed 's/\[t\]//g' | awk 'BEGIN{FS=" "};{if($0 ~ /^ *0/){print $0}}' | sort -Vr | head -1)
+nextflow run hoelzer-lab/ribap -r $REVISION --help
+
+# Run with RAxML tree calculation and specified output dir:
+nextflow run hoelzer-lab/ribap -r $REVISION --fasta '*.fasta' --tree --outdir ~/ribap -w work
+
+# Run with optional reference Genbank file to guide Prokka annotation, ATTENTION: this will use the additional reference file for every input genome!
+nextflow run hoelzer-lab/ribap -r $REVISION --fasta '*.fasta' --reference GCF_000007205.1_ASM720v1_genomic.gbff --outdir ~/ribap -w work
+
+# Use list parameter to provide genome FASTAs and corresponding reference GenBank files in CSV format
+nextflow run hoelzer-lab/ribap -r $REVISION --list --fasta genomes.csv --reference refs.csv --outdir ~/ribap -w work
+
+# genomes.csv:
+#
+# genome1,genome1.fasta
+# genome2,genome2.fasta
+# genome3,genome3.fasta
+
+# refs.csv
+#
+# genome1,ref.gbff
+# genome2,ref.gbff
+# 
+# Here, genome1 and genome2 will additionally use information from ref.gbff in Prokka annotatio while genome3 will be annotated w/o additional reference information
+```
 
-* runs with the workflow manager `nextflow` using `docker` or `conda`
-* this means all programs are automatically pulled via `docker` or `conda`
-* only `docker` or `conda` and `nextflow` need to be installed (per default `docker` is used)
+# Installation
 
-### Nextflow
-Needed in both cases (`conda`, `docker`)
+* runs with the workflow manager `nextflow` using `docker` or `singularity` or `conda`
+* this means all programs are automatically pulled via `docker`, `singularity`, or `conda`
+* only `docker` or `sinularity` or `conda` and `nextflow` need to be installed (per default `docker` is used)
+
+## Nextflow
+Needed in all cases (`conda`, `docker`, `singularity`)
 ```bash
 sudo apt-get update
 sudo apt install -y default-jre
 curl -s https://get.nextflow.io | bash 
 sudo mv nextflow /bin/
 ```
 
-### Using Conda
+## Using Conda
 
 Just copy the commands and follow the installation instructions. Let the installer configure `conda` for you. You need to specify `-profile conde` to run the pipeline with conda support.  
 ```bash
@@ -55,9 +94,9 @@ bash Miniconda3-latest-Linux-x86_64.sh
 ```
 See [here](https://docs.conda.io/en/latest/miniconda.html) if you need a different installer besides Linux used above. 
 
-### Using Docker
+## Using Docker
 
-#### Easy 
+### Easy 
 If you dont have experience with bioinformatic tools just copy the commands into your terminal to set everything up:
 ```bash
 sudo apt-get install -y docker-ce docker-ce-cli containerd.io
@@ -66,7 +105,7 @@ sudo usermod -a -G docker $USER
 * restart your computer
 * try out the installation by entering the following
 
-#### Experienced
+### Experienced
 
 **Dependencies**
 
@@ -81,39 +120,6 @@ sudo usermod -a -G docker $USER
 * move or add the nextflow executable to a bin path
 * add docker to your User group via `sudo usermod -a -G docker $USER`
 
-# Execution examples
-
-```bash
-# Get or update the workflow:
-nextflow pull hoelzer-lab/ribap
-
-# Run a specific release.
-# Get newest release version automatically or choose one yourself
-REVISION=$(nextflow info hoelzer-lab/ribap | sed 's/ [*]//' | sed 's/ //g' | sed 's/\[t\]//g' | awk 'BEGIN{FS=" "};{if($0 ~ /^ *0/){print $0}}' | sort -Vr | head -1)
-nextflow run hoelzer-lab/ribap -r $REVISION --help
-
-# Run with RAxML tree calculation and specified output dir:
-nextflow run hoelzer-lab/ribap -r $REVISION --fasta '*.fasta' --tree --outdir ~/ribap -w work
-
-# Run with optional reference Genbank file to guide Prokka annotation, ATTENTION: this will use the additional reference file for every input genome!
-nextflow run hoelzer-lab/ribap -r $REVISION --fasta '*.fasta' --reference GCF_000007205.1_ASM720v1_genomic.gbff --outdir ~/ribap -w work
-
-# Use list parameter to provide genome FASTAs and corresponding reference GenBank files in CSV format
-nextflow run hoelzer-lab/ribap -r $REVISION --list --fasta genomes.csv --reference refs.csv --outdir ~/ribap -w work
-
-# genomes.csv:
-#
-# genome1,genome1.fasta
-# genome2,genome2.fasta
-# genome3,genome3.fasta
-
-# refs.csv
-#
-# genome1,ref.gbff
-# genome2,ref.gbff
-# 
-# Here, genome1 and genome2 will additionally use information from ref.gbff in Prokka annotatio while genome3 will be annotated w/o additional reference information
-```
 
 # Flowchart
 ![chart](figures/dag.png)