example dataset

Author: rwittler

.github/workflows/publish-container.yml

@@ -40,7 +40,7 @@ jobs:
           tags: |
             # set latest tag for default branch
             type=raw,value=latest
-            type=raw,value=v1.0.3
+            type=raw,value=v1.0.4
       # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
       # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
       # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.

clowm/CHANGELOG.md

@@ -1,5 +1,18 @@
 # SANS Changelog
 
+
+
+## v1.0.4 [2025-02-11]
+
+### Fixed
+
+- last codon in coding sequence translation got lost
+
+### Added
+
+- example data set
+
+
 ## v1.0.3 [2025-02-07]
 
 ### Fixed

clowm/CITATIONS.md

@@ -12,3 +12,10 @@ In: Huber, K. and Gusfield, D. (eds.) Proceedings of WABI 2019. LIPIcs. 143, Sch
 # Splitstree
 
 Huson, D. H. and Bryant, D.: [Application of Phylogenetic Networks in Evolutionary Studies](https://doi.org/10.1093/molbev/msj030), Mol. Biol. Evol., 23(2):254-267 (2006).
+
+# Example dataset
+
+Shapiro, B. J., Levade, I., Kovacikova, G., Taylor, R. K. and Almagro-Moreno S.: [Origins of pandemic Vibrio cholerae from environmental gene pools](https://doi.org/10.1038/nmicrobiol.2016.240), Nat. Microbiol., 2(3):16240 (2017).
+
+preprocessed with [ORFfinder](https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/)
+

clowm/clowm_info.json

@@ -8,5 +8,11 @@
   "dois": [
     "10.1093/bioinformatics/btab444",
     "10.1186/s13015-020-00164-3"
-  ]
-}
+  ],
+  "exampleParameters": {
+    "inputfile": "s3://workflow-exampledata/sans-ambage/example2/",
+    "file_of_files": "s3://workflow-exampledata/sans-ambage/example2/cholerae.kmt",
+    "translate": true,
+    "label": "s3://workflow-exampledata/sans-ambage/example2/mapping.tsv"
+  }
+}

clowm/main.nf

@@ -8,7 +8,7 @@ params.file_of_files = "$projectDir/NO_FILE3"
 params.blacklist = "$projectDir/NO_FILE4"
 
 process sans {
-  container "ghcr.io/gi-bielefeld/sans:v1.0.3"
+  container "ghcr.io/gi-bielefeld/sans:v1.0.4"
   publishDir params.outdir, mode: 'symlink'
   debug false
   label 'highmemMedium'

clowm/tryitout.png

@@ -9,6 +9,8 @@ To ease the application of SANS for unexperienced users, the CloWM version of SA
 | <img src="https://raw.githubusercontent.com/gi-bielefeld/sans/clowm-integration/clowm/simple.png" style="border:0;" alt="simple" height="30"/> | | Select the input and output folders and run SANS with default parameters. |
 | <img src="https://raw.githubusercontent.com/gi-bielefeld/sans/clowm-integration/clowm/advanced.png" style="border:0;" alt="advanced" height="30"/> | | If your input are **reads** or **coding sequences**, or if you want to **beautify the output**, switch the parameter view to "advanced". |
 | <img src="https://raw.githubusercontent.com/gi-bielefeld/sans/clowm-integration/clowm/expert.png" style="border:0;" alt="expert" height="30"/> | | This parameter view provides further options, such as bootstrapping. |
+| | | |
+| <img src="https://raw.githubusercontent.com/gi-bielefeld/sans/clowm-integration/clowm/tryitout.png" style="border:0;" alt="expert" height="30"/> | | The launch page also provides a simple example. (See "Citations" for details.)|
 
 
 </br>