diff --git a/CHANGELOG.md b/CHANGELOG.md index 3fc13e42..a5543298 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/README.md b/README.md index 0de52296..4e016ac4 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ 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 @@ -37,4 +37,4 @@ Contributions to the pipeline is more than welcome. Please use the [CONTRIBUTING ## License -Jasen is released under the GPLv3 license. \ No newline at end of file +Jasen is released under the GPLv3 license. diff --git a/assets/test_data/samplelist_nanopore.csv b/assets/test_data/samplelist_nanopore.csv new file mode 100644 index 00000000..72d2f064 --- /dev/null +++ b/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 diff --git a/assets/test_data/sequencing_data/saureus_nanopore_1k/saureus_nanopore_1k.fastq.gz b/assets/test_data/sequencing_data/saureus_nanopore_1k/saureus_nanopore_1k.fastq.gz new file mode 100644 index 00000000..600d2aa1 Binary files /dev/null and b/assets/test_data/sequencing_data/saureus_nanopore_1k/saureus_nanopore_1k.fastq.gz differ diff --git a/docs/source/install.md b/docs/source/install.md index 65f1110d..21ff3b29 100644 --- a/docs/source/install.md +++ b/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