Merge branch 'main' of github.com:genepi/mtdna-server-2

README.md

@@ -7,6 +7,12 @@ mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic an
 
 ![image](docs/images/report.png)
 
+### Documentation
+The documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). 
+
+## Citation
+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 [v2.1.15](../../releases/tag/v2.1.15) - Add option for min mean coverage
@@ -21,76 +27,4 @@ Release [v2.1.11](../../releases/tag/v2.1.11) - Improve QC command, update to la
 
 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?
-We want to steadily improve mtDNA-Server 2. If your files are not working, please feel free to create a issue or contact [[Sebastian](mailto:[email protected])] directly. 
-
-## How to execute mtDNA-Server 2?
-mtDNA-Server 2 is available as a **hosted web-service** at the Medical University of Innsbruck or as a **Nextflow pipeline**.
-
-## Web Service
-
-mtDNA-Server 2 is hosted as a **free** service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform.
-
-### Documentation
-
-The web-service documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). 
-
-## Nextflow Pipeline
-To run mtDNA-Server 2 via Nextflow, please execute the following steps. 
-
-### Quick Start
-
-1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) (>=22.10.4)
-
-2. Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm. 
-```
-nextflow run genepi/mtdna-server-2 -r v2.X.XX -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.X.XX -c <your-config-file> -profile <docker,singularity,slurm>
-```
-
-### Parameters
-The following parameters can be set in the configuration file. 
-| Parameter            | Default Value        | Comment        |
-|----------------------|--------------|----------------|
-| project              | null         | Project name (required)   |
-| files                | null         | Input BAM files (required) |
-| mode                 | fusion       | Mode of operation (mutserve,mutect2,fusion) |
-| detection_limit      | 0.02         | Detection limit for heteroplasmic sites |
-| coverage_estimation  | on           | Coverage estimation enabled |
-| subsampling          | off          | Subsampling on/off |
-| subsampling_coverage | 2000         | Subsampling coverage |
-| mapQ                 | 20           | Mapping quality threshold |
-| baseQ                | 20           | Base quality threshold |
-| alignQ               | 30           | Alignment quality threshold |
-| min_mean_coverage               | 50           | Min Mean coverage |
-| output               | null         | Specific Output folder   |
-
-## Development
-```
-git clone https://github.com/genepi/mtdna-server-2
-cd mtdna-server-2
-docker build -t genepi/mtdna-server-2 . # don't ignore the dot
-nextflow run main.nf -profile test,development
-```
-
-## Publication
-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.
-
-
-## Contact
-
-This software was developed at the [Institute of Genetic Epidemiology](https://genepi.i-med.ac.at/), [Medical University of Innsbruck](https://i-med.ac.at/)
-
-![](https://avatars2.githubusercontent.com/u/1942824?s=30) [Sebastian Schoenherr](mailto:[email protected]) ([@seppinho](https://twitter.com/seppinho))
-
-![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:[email protected]) ([@whansi](https://twitter.com/whansi))
-
-![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:[email protected]) ([@lukfor](https://twitter.com/lukfor))
-
-## License
 
-MIT Licensed.

cloudgene.yaml

@@ -126,7 +126,7 @@ workflow:
     - id: min_mean_coverage
       description: Minimal Mean Coverage 
       type: number
-      visible: false
+      visible: true
       value: 50  
 
     - id: baseQ
@@ -159,4 +159,4 @@ workflow:
       description: Auxiliary Files
       type: local-folder
       download: true
-      temp: false
+      temp: false

workflows/mtdna_server_2.nf

@@ -235,7 +235,7 @@ workflow.onComplete {
                 to "${params.user.email}"
                 from "${params.service.email}"
                 subject "[${params.service.name}] Job ${params.project} failed."
-                body "Hi ${params.user.name}, your job failed :(. Logs can be accessed at ${params.service.url}/index.html#!jobs/${params.project}"
+                body "Dear ${params.user.name}, your job has ${statusMessage}. More details can be found at the following link: ${params.service.url}/index.html#!jobs/${params.project}"
 
             }
         }
@@ -250,11 +250,11 @@ workflow.onComplete {
         sendMail{
             to "${params.user.email}"
             from "${params.service.email}"
-            subject "[${params.service.name}] Job ${params.project} is complete."
-            body "Hi ${params.user.name}, your job completed successfully and can be accessed at ${params.service.url}/index.html#!jobs/${params.project}"
+            subject "[${params.service.name}] Job ${params.project} is complete"
+            body "Dear ${params.user.name}, \n your mtDNA-Server 2 job has finished succesfully.\n You can download the results from the following link: ${params.service.url}/index.html#!jobs/${params.project}"
         }
-        report.ok("Sent email notification to <b>${params.user.email}</b>")
+        println "::message:: " + "Sent email notification to <b>${params.user.email}</b>"
     } else {
 
     }
-}
+}