Output Documentation

CITATIONS.md

@@ -18,6 +18,10 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: https://10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [NET2COMMUNITIES](https://github.com/pangenome/pggb/blob/master/scripts/net2communities.py)
+
+  > Traag, VA, Waltman, L & van Eck, NJ. From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep 9, 5233 (2019). https://doi.org/10.1038/s41598-019-41695-z.
+
 - [ODGI](https://pubmed.ncbi.nlm.nih.gov/35552372/)
 
   > Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. ODGI: understanding pangenome graphs. Bioinformatics. Volume 38. Issue 13. July 2022. Pages 3319–3326. https://doi.org/10.1093/bioinformatics/btac308.

README.md

@@ -26,8 +26,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 - All versus all alignment (`WFMASH`)
 - Graph induction (`SEQWISH`)
 - Graph normalization (`SMOOTHXG`)
@@ -93,7 +91,7 @@ Many thanks to all who have helped out and contributed along the way, including
 | Name                                                       | Affiliation                                                                                                                                                                                                                                                                                                                                                                       |
 | ---------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | [Philipp Ehmele](https://github.com/imipenem)              | [Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany](https://www.helmholtz-muenchen.de/icb/index.html)                                                                                                                                                                                                                                                |
-| [Gisela Gabernet](https://github.com/ggabernet)            | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br> [Department of Pathology, Yale School of Medicine, New Haven, USA](https://medicine.yale.edu/pathology/)                                                                                                                                                                                                    |
+| [Gisela Gabernet](https://github.com/ggabernet)            | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br> [Department of Pathology, Yale School of Medicine, New Haven, USA](https://medicine.yale.edu/pathology/)                                                                                      |
 | [Erik Garrison](https://github.com/ekg)                    | [The University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/)                                                                                                                                                                                                                                                                              |
 | [Andrea Guarracino](https://github.com/AndreaGuarracino)   | [Genomics Research Centre, Human Technopole, Milan, Italy](https://humantechnopole.it/en/)                                                                                                                                                                                                                                                                                        |
 | [Friederike Hanssen](https://github.com/FriederikeHanssen) | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br> [Biomedical Data Science, Department of Computer Science, University of Tübingen, Germany](https://uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department/) |

conf/modules.config

@@ -418,7 +418,7 @@ process {
     }
 
     withName: ODGI_SQUEEZE {
-        ext.prefix = {"${meta.id}.squeeze.unchop.Ygs"}
+        ext.prefix = {"${meta.id}.squeeze"}
         publishDir = [
             path: { "${params.outdir}/FINAL_ODGI" },
             mode: params.publish_dir_mode,