From a1a20cdee6765029ad89409b4732524bc4373658 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Sat, 28 Dec 2024 15:44:25 +0100 Subject: [PATCH 1/5] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 658c571..0060098 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ 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:sebastian.schoenherr@i-med.ac.at)] directly. +We want to steadily improve mtDNA-Server 2. If your files are not working, please feel free to create a [issue](https://github.com/genepi/mtdna-server-2/issues). ## 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**. @@ -33,7 +33,7 @@ mtDNA-Server 2 is hosted as a **free** service on our [mitoverse](https://mitove ### Documentation -The web-service documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). +The 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. From f6fa7521c358561282b74fffefa4d56cb2b484ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Sat, 28 Dec 2024 16:46:16 +0100 Subject: [PATCH 2/5] Update README.md --- README.md | 78 +++++-------------------------------------------------- 1 file changed, 6 insertions(+), 72 deletions(-) diff --git a/README.md b/README.md index 0060098..a118c42 100644 --- a/README.md +++ b/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](https://github.com/genepi/mtdna-server-2/issues). - -## 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 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, -``` -### 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 -profile -``` - -### 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:sebastian.schoenherr@i-med.ac.at) ([@seppinho](https://twitter.com/seppinho)) - -![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:hansi.weissensteiner@i-med.ac.at) ([@whansi](https://twitter.com/whansi)) - -![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:lukas.forer@i-med.ac.at) ([@lukfor](https://twitter.com/lukfor)) - -## License -MIT Licensed. From 576ba12e877af8bb1a8474dedd1a68b9cc41f39c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Sat, 28 Dec 2024 18:34:53 +0100 Subject: [PATCH 3/5] Update mtdna_server_2.nf --- workflows/mtdna_server_2.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf index 233acca..62c68d9 100644 --- a/workflows/mtdna_server_2.nf +++ b/workflows/mtdna_server_2.nf @@ -253,8 +253,8 @@ workflow.onComplete { 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}" } - report.ok("Sent email notification to ${params.user.email}") + println "::message:: " + "Sent email notification to ${params.user.email}" } else { } -} \ No newline at end of file +} From 62b465641694177d4b0d7a6b33bc664e3c8be6f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Sat, 28 Dec 2024 18:42:32 +0100 Subject: [PATCH 4/5] Update mtdna_server_2.nf --- workflows/mtdna_server_2.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf index 62c68d9..0e8c923 100644 --- a/workflows/mtdna_server_2.nf +++ b/workflows/mtdna_server_2.nf @@ -235,7 +235,7 @@ workflow.onComplete { to "${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}" } } @@ -250,8 +250,8 @@ 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}" } println "::message:: " + "Sent email notification to ${params.user.email}" } else { From c8ac8ab05fa12e8059ad815c17b94314582e3b7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Sat, 28 Dec 2024 18:44:49 +0100 Subject: [PATCH 5/5] Update cloudgene.yaml --- cloudgene.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cloudgene.yaml b/cloudgene.yaml index 13288dc..d3864ae 100644 --- a/cloudgene.yaml +++ b/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 \ No newline at end of file + temp: false