Merge branch 'master' of github.com:replikation/What_the_Phage

CITATION.cff

@@ -0,0 +1,44 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Marquet"
+  given-names: "Mike"
+- family-names: "Hölzer"
+  given-names: "Martin"
+- family-names: "Pletz"
+  given-names: "Mathias W."
+- family-names: "Viehweger"
+  given-names: "Adrian"
+- family-names: "Makarewicz"
+  given-names: "Oliwia"
+- family-names: "Ehricht"
+  given-names: "Ralf"
+- family-names: "Brandt"
+  given-names: "Christian"
+title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences"
+version: v1.2.0
+date-released: 2022-11-18
+url: "https://github.com/replikation/What_the_Phage"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Marquet"
+    given-names: "Mike"
+  - family-names: "Hölzer"
+    given-names: "Martin"
+  - family-names: "Pletz"
+    given-names: "Mathias W."
+  - family-names: "Viehweger"
+    given-names: "Adrian"
+  - family-names: "Makarewicz"
+    given-names: "Oliwia"
+  - family-names: "Ehricht"
+    given-names: "Ralf"
+  - family-names: "Brandt"
+    given-names: "Christian"
+  doi: "10.1093/gigascience/giac110"
+  journal: "Gigascience"
+  month: 11
+  title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences"
+  year: 2022
+  issn: 2047-217X

README.md

@@ -8,7 +8,7 @@
 ![](https://img.shields.io/badge/uses-docker-blue.svg)
 ![](https://img.shields.io/badge/uses-singularity-yellow.svg)
 
-[![Generic badge](https://img.shields.io/badge/Preprint-bioRxiv-red.svg)](https://www.biorxiv.org/content/10.1101/2020.07.24.219899v2)
+[![Generic badge](https://img.shields.io/badge/Publication-Gigascience-blueviolet.svg)](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac110/6833029)
 [![Generic badge](https://img.shields.io/badge/Documentation-available-purple.svg)](https://mult1fractal.github.io/wtp-documentation/)
 
 [![Twitter Follow](https://img.shields.io/twitter/follow/gcloudChris.svg?style=social)](https://twitter.com/gcloudChris) 
@@ -22,13 +22,13 @@
   * These are extensively tested release versions of WtP
   * [releases of WtP are listed here](https://github.com/replikation/What_the_Phage/releases)  
 
-## Preprint:
+## Publication:
 
 > **What the Phage: A scalable workflow for the identification and analysis of phage sequences**
 >
 > M. Marquet, M. Hölzer, M. W. Pletz, A. Viehweger, O. Makarewicz, R. Ehricht, C. Brandt
 >
-> doi: https://doi.org/10.1101/2020.07.24.219899
+> doi: https://doi.org/10.1093/gigascience/giac110
 
 # What is this repo
 

submodule_report/Heatmap_table.Rmd

@@ -94,8 +94,8 @@ div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
 # Open your Linux-Terminal     
 mkdir contigs_of_interest 
 cd  contigs_of_interest  
-# Copy the downloaded Phage prediction by contig table to the contig_IDs_of_interest -folder  
-# Copy the input_fasta to the contig_IDs_of_interest -folder  
+# Copy the downloaded Phage prediction by contig table to the contigs_of_interest -folder  
+# Copy the input_fasta to the contigs_of_interest -folder  
 cp WtP_results/your_sample/Input_fasta/your_input_fasta.fa.gz /foo/bar/contigs_of_interest  
 # Get contig IDs of interest  
 tail -n+2 final_report.utf8.csv | tr -d '"' | cut -f2 -d"," > contig_IDs_of_interest.txt  
@@ -110,4 +110,4 @@ seqkit grep --pattern-file contig_IDs_of_interest.txt your_input_fasta.fa.gz > c
 
 
 
-<a href="#top">Back to top</a>
+<a href="#top">Back to top</a>