update README

README.md

@@ -1,15 +1,17 @@
 # Calculation of the Percentage Of Conserved Proteins
 
-![](https://img.shields.io/badge/nextflow-20.10.0-brightgreen)
+![](https://img.shields.io/badge/nextflow->=20.01.0-brightgreen)
 ![](https://img.shields.io/badge/uses-ruby-red)
-![](https://img.shields.io/badge/can_use-conda-yellow.svg)
+![](https://img.shields.io/badge/can_use-conda/mamba-yellow.svg)
 ![](https://img.shields.io/badge/can_use-docker-blue.svg)
 ![](https://img.shields.io/badge/can_use-singularity-orange.svg)
 ![](https://img.shields.io/badge/licence-GLP3-lightgrey.svg)
 
 [![Twitter Follow](https://img.shields.io/twitter/follow/martinhoelzer.svg?style=social)](https://twitter.com/martinhoelzer) 
 
-__Update 2023: Re-implementation as a [Nextflow pipeline](nextflow.io). Please feel free to report any [issues](https://github.com/hoelzer/pocp/issues)!__
+__Update 2023/05: Re-implementation as a [Nextflow pipeline](nextflow.io). Please feel free to report any [issues](https://github.com/hoelzer/pocp/issues)!__
+
+__Update 2023/10: Now using [Diamond](https://www.nature.com/articles/s41592-021-01101-x) instead of Blast for protein alignments. Thx [@michoug](https://github.com/michoug) for the Pull Request.__
 
 As input use one amino acid sequence FASTA file per genome such as provided by
 [Prokka](https://github.com/tseemann/prokka) or genome FASTA files which will be then annotated via [Prokka](https://github.com/tseemann/prokka). 
@@ -26,26 +28,25 @@ nextflow pull hoelzer/pocp
 # check availble release versions and development branches
 nextflow info hoelzer/pocp 
 
-# get the help page and define a release version
-nextflow run hoelzer/pocp -r 2.0.0 --help
+# get the help page and define a release version. ATTENTION: use latest version. 
+nextflow run hoelzer/pocp -r 2.1.0 --help
 
 # example with genome files as input, performing a local execution and using Docker
-nextflow run hoelzer/pocp -r 2.0.0 --genomes 'example/*.fasta' -profile local,docker
+nextflow run hoelzer/pocp -r 2.1.0 --genomes 'example/*.fasta' -profile local,docker
 
 # example with protein FASTA files as input (e.g. from Prokka pre-calculated), performing a SLURM execution and using conda
-nextflow run hoelzer/pocp -r 2.0.0 --proteins 'example/*.faa' -profile slurm,conda
+nextflow run hoelzer/pocp -r 2.1.0 --proteins 'example/*.faa' -profile slurm,conda
 ```
 
-The final output (`pocp-matrix.tsv`) should look like this (here, the resulting `pocp-matrix.tsv` was imported into LibreOffice and formated):
+The final output (`pocp-matrix.tsv`) should look like this (here, the resulting TSV was imported into Numbers on MacOS):
 
 ![Example output](example_output.png)
 
-If needed, the following parameters used for filtering the `blast` results can be
+If needed, the following parameters used for filtering the `diamond` results (blastp mode) can be
 adjusted:
 
 ```bash
 --evalue 1e-5
 --seqidentity 0.4
 --alnlength 0.5
 ```
-