Prepare release v2.1.10

genepi · May 29, 2024 · 3ce86b1 · 3ce86b1
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diff --git a/.nf-test.log b/.nf-test.log
@@ -0,0 +1,24 @@
+May-29 14:15:49.869 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.0-rc1
+May-29 14:15:49.876 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/mitocalling.nf.test@1a7901f2, --verbose, --debug]
+May-29 14:15:50.293 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
+May-29 14:15:50.294 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /Users/seb/repositories/mtdna-server-2/nf-test.config...
+May-29 14:15:50.474 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 19 files from directory /Users/seb/repositories/mtdna-server-2 in 0.02 sec
+May-29 14:15:50.475 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests.
+May-29 14:15:50.475 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/seb/repositories/mtdna-server-2/tests/mitocalling.nf.test@1a7901f2]
+May-29 14:15:50.475 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/Users/seb/repositories/mtdna-server-2/tests/mitocalling.nf.test'.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '7e071ab6: Runs with single BAM file and mutserve' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '43f21514: Runs with BAM file including different header contigs' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '9a9b8647: Runs with single BAM file and mutect2' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '174031f7: Runs with two files and one goes through QC' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '5e87182d: Runs with 6 samples provided as testdata with mutserve' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '80a87f45: Runs with 6 samples provided as testdata with mutect2' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '37e8e015: Runs with 6 samples provided as testdata with fusion' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test 'e9c8ac0f: Run sample without readgroup and mutect2' skipped.
+May-29 14:15:50.848 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '1a7901f2: Run sample with complex ref tag and mutect2'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+May-29 14:16:15.996 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/seb/repositories/mtdna-server-2/tests/mitocalling.nf.test.snap'
+May-29 14:16:16.001 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Run sample with complex ref tag and mutect2' match.
+May-29 14:16:16.001 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '1a7901f2: Run sample with complex ref tag and mutect2' finished. status: PASSED
+May-29 14:16:16.002 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: true, skipped tests: true, failed tests: false
+May-29 14:16:16.002 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!
diff --git a/README.md b/README.md
@@ -17,15 +17,19 @@ mtDNA-Server 2 is hosted as a **free** service on our [mitoverse](https://mitove
 
 ### Documentation
 
-Documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/).
+Documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). 
 
 ![image](docs/images/workflow.png)
 
+We want to steadily improve mtDNA-Server 2. If your files are not working, please create a issue or contact [[Sebastian](mailto:[email protected])] directly. 
+
+
+### Version History
+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.
 
 ## 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.
 
-
 ## Local Execution
 To run mtDNA-Server 2 locally, please execute the following steps. 
 
@@ -35,12 +39,12 @@ To run mtDNA-Server 2 locally, 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 v2.1.9 -profile test,<docker,singularity,slurm>
+nextflow run genepi/mtdna-server-2 -r v2.1.10 -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 v2.1.9 -c <your-config-file> -profile docker
+nextflow run genepi/mtdna-server-2 -r v2.1.10 -c <your-config-file> -profile docker
 ```
 
 ### Development

diff --git a/cloudgene.yaml b/cloudgene.yaml
@@ -2,7 +2,7 @@ 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>"
 
-version: v2.1.9
+version: v2.1.10
 website: https://mitoverse.readthedocs.io/
 category:
 
@@ -114,7 +114,7 @@ workflow:
     - id: subsampling
       description: Coverage Subsampling
       type: list
-      value: off
+      value: on
       values:
         off: No subsampling
         on: Subsample to 2000x 

diff --git a/nextflow.config b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
     name                                  = 'mtDNA-Server 2'
-    version                               = 'v2.1.9'
+    version                               = 'v2.1.10'
     description                           = 'mtDNA Variant Calling'
     author                                = 'Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer'
     homePage                              = 'https://github.com/genepi/mtdna-server-2'
@@ -23,7 +23,7 @@ params {
     alignQ                 = 30
     coverage_estimation    = "on"
     max_samples            = 0
-    subsampling            = "off"
+    subsampling            = "on"
     subsampling_coverage   = 2000