Prepare release v.2.1.11

genepi · May 31, 2024 · 5e6b019 · 5e6b019
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diff --git a/README.md b/README.md
@@ -23,12 +23,12 @@ To run mtDNA-Server 2 via Nextflow, please execute the following steps.
 
 2. Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm. 
 ```
-nextflow run genepi/mtdna-server-2 -r v2.1.10 -profile test,<docker,singularity,slurm>
+nextflow run genepi/mtdna-server-2 -r v2.1.11 -profile test,<docker,singularity,slurm>
 ```
 ### Run Pipeline on own data
 To run mtDNA-Server 2 on your own data, create a [config file](tests/test_mitohpc_fusion.config) and run the following command:
 ```
-nextflow run genepi/mtdna-server-2 -r v2.1.10 -c <your-config-file> -profile docker
+nextflow run genepi/mtdna-server-2 -r v2.1.11 -c <your-config-file> -profile docker
 ```
 
 ## Documentation
@@ -41,6 +41,8 @@ Documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-serv
 Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. [mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics](https://doi.org/10.1093/nar/gkae296). Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
 
 ### Version History
+Release [v2.1.11](../../releases/tag/v2.1.11) - Improve QC command, update to latest mutserve v2.0.1.
+
 Release [v2.1.10](../../releases/tag/v2.1.10) - Improved mutect2 support: create missing RG tags, write inidividual reference sequence on the fly, support complex ref tags.
 
 ## Are your files not working?

diff --git a/cloudgene.yaml b/cloudgene.yaml
@@ -1,8 +1,8 @@
 id: mtdna-server-2
 name: mtDNA-Server 2 - Mitochondrial Variant Calling 
-description: "You can upload data in BAM format and the application return homoplasmic and heterplasmic sites.<br><br>No dataset at hand? No problem, download and extract our example dataset: <a href=\"https://mitoverse.i-med.ac.at/downloads/6-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 6-samples.zip</a><br><br>"
+description: "A free web service to analyze your mtDNA NGS data.<br>Feel free to <a href=\"https://github.com/genepi/mtdna-server-2/?tab=readme-ov-file#contact\">contact us</a> if you have issues running the pipeline.<br><br>No dataset at hand? No problem, download and extract our example dataset: <a href=\"https://mitoverse.i-med.ac.at/downloads/6-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 6-samples.zip</a><br><br>"
 
-version: v2.1.10
+version: v2.1.11
 website: https://mitoverse.readthedocs.io/
 category:
 

diff --git a/environment.yml b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-mito-calling
+name: mtdna-server-2
 channels:
   - conda-forge
   - bioconda

diff --git a/nextflow.config b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
     name                                  = 'mtDNA-Server 2'
-    version                               = 'v2.1.10'
+    version                               = 'v2.1.11'
     description                           = 'mtDNA Variant Calling'
     author                                = 'Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer'
     homePage                              = 'https://github.com/genepi/mtdna-server-2'
@@ -45,7 +45,7 @@ params {
 profiles {
     debug { process.beforeScript          = 'echo $HOSTNAME' }
 
-    process.container                 = 'quay.io/genepi/mtdna-server-2:v2.1.10'
+    process.container                 = 'quay.io/genepi/mtdna-server-2:v2.1.11'
     docker.enabled                    = true
     docker.userEmulation              = true
     singularity.enabled               = false