297 add nanopore test data (#337)

* add ONT test data and samplelist for ONT

* force adding long-reads test data

CHANGELOG.md

@@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added long-read test data (S. aureus)
+- Added `samplelist_nanopore.csv` for running long-read test data
+- Added location of documentation to `README` 
 - Added `cdmDir` to config
 
 ### Fixed

README.md

@@ -29,12 +29,12 @@ See the documentation for installation instructions.
 
 ## Documentation
 
-The documentation is abailable for the latest stable release.
+The documentation `docs/source` is available for the latest stable release.
 
 ## Contributing
 
 Contributions to the pipeline is more than welcome. Please use the [CONTRIBUTING](CONTRIBUTING.md) file for details.
 
 ## License
 
-Jasen is released under the GPLv3 license.
+Jasen is released under the GPLv3 license.

assets/test_data/samplelist_nanopore.csv

@@ -0,0 +1,2 @@
+id,platform,sequencing_run,read1
+test_mecA,nanopore,20231017_1501_MN39800_ARA658_5ab3fe12,PATH_TO_JASEN/assets/test_data/sequencing_data/saureus_nanopore_1k/saureus_nanopore_1k.fastq.gz

docs/source/install.md

@@ -67,9 +67,10 @@ When analysing Nanopore data:
 * Edit the `ext.args` for Medaka: specify the model with flag `-m`. Currently it is set to `r941_min_sup_g507`, but one should always set it based on how the data was produced. More about choosing the right model can be found [here](https://github.com/nanoporetech/medaka#models).
 
 ### Test data
-Source: `assets/test_data/samplelist.csv`
+Source: `assets/test_data/samplelist*.csv`
 
-* Edit the read1 and read2 columns in `assets/test_data/samplelist.csv`
+* For short reads produced with Illumina or IonTorrent technology, edit the read1 and read2 columns in `assets/test_data/samplelist.csv`
+* For long reads produced with ONT technology, edit the read1 column in `assets/test_data/samplelist_nanopore.csv`
 
 ## Setting up temp directories