Merge pull request #900 from ScilifelabDataCentre/develop

Update W42

content/english/pathogens/monkeypox.md

@@ -81,6 +81,7 @@ These tools have been adapted/developed for use with the monkeypox virus. They c
 - [WHO - Q&A related to monkeypox](https://www.who.int/news-room/questions-and-answers/item/monkeypox)
 - [ECDC & WHO -  Monkeypox report](https://monkeypoxreport.ecdc.europa.eu/)
 - [ECDC - Monkeypox infection prevention and control guidance](https://www.ecdc.europa.eu/en/publications-data/monkeypox-infection-prevention-and-control-guidance-primary-and-acute-care)
+- [ECDC update on the outbreak](https://www.ecdc.europa.eu/en/publications-data/monkeypox-multi-country-outbreak-second-update) from October 2022
 - [ECDC - Factsheet on monkeypox for health professionals](https://www.ecdc.europa.eu/en/all-topics-z/monkeypox/factsheet-health-professionals)
 - [EMA response to the monkeypox public health emergency](https://www.ema.europa.eu/en/news/ema-response-monkeypox-public-health-emergency)
 - [P1 cultured virus from a monkeypox positive patient available from European Virus Archive](https://www.european-virus-archive.com/virus/monkeypox-virus-mpxv2022nl001-animal-human-2022-netherlands-mpxv2022nl001)

content/english/resources-subprojects/gms-arctic.md

@@ -14,10 +14,10 @@ resource_info:
     contact: "Sofia Stamouli<br>Bioinformatician<br>Email: [[email protected]](mailto:[email protected])"
 ---
 
-A pipeline for taxonomic profiling of shotgun metagenomic data. It is currently in development and does not yet have any stable releases.
+A pipeline for bioinformatical analysis of SARS-CoV-2 data was developed within Genomics Medicine Sweden during the spring of 2021. The pipeline extends on the analysis developed by the international collaboration ArticNetwork and the COG-UK consortium. It is currently in clinical use across Sweden and is continually updated with the latest SARS-CoV-2 variants.
 
-The pipeline supports metagenomic data generated both from Illumina and Nanopore sequencing technology. It performs in-parallel taxonomic profiling with multiple taxonomic classifiers against multiple databases and produces standardised output tables. In addition, it performs quality control and optional read pre-processing (adapter trimming, low-complexity filtering and host read removal).
+The pipeline performs typing of SARS-CoV-2 data using both the Pangolin and Nextstrain classification systems. In addition, it also runs quality control, variant calling and supplies a genome consensus sequence for each sample. The pipeline has two different modes depending on the sequencing technology used, one for short read data such as Illumina sequencing data, and the other for long read data generated from Nanopore sequencing.
 
-The pipeline is written in Nextflow DSL-2 workflow manager and it uses Docker/Singularity containers.
+The pipeline is written in Nextflow workflow manager and is already set up to run with conda environments, docker or singularity containers. Support has also been set up for execution with various job schedulers such as slurm, lsf, gls and sge, and is easily adapted for other systems through the Nextflow set up.
 
 For more information on the [Pandemic Laboratory Preparedness resources](/resources/) associated with this subproject, see [Genomic Pandemic Preparedness Portfolio (G3P)](/resources/g3p/), [Rapid establishment of comprehensive laboratory pandemic preparedness – RAPID-SEQ](/resources/rapid-seq/), and [Next generation clinical virology](/resources/ng_clinical_virology/). Please also refer to other associated subprojects; [taxprofiler](/resources-subprojects/taxprofiler/) and [SC2 Reporter](/resources-subprojects/sc2reporter/).