Simplified the instructions to test the pipeline

.github/workflows/ci.yml

@@ -48,10 +48,6 @@ jobs:
         run: |
           nextflow secrets set NCBI_API_KEY ${{ secrets.NCBI_API_KEY }}
 
-      - name: Download test data
-        run: |
-          curl https://tolit.cog.sanger.ac.uk/test-data/resources/genomeassembly/genomeassembly_test_data.tar.gz | tar xzf -
-
       - name: Setup apptainer
         uses: eWaterCycle/setup-apptainer@main
 

docs/usage.md

@@ -86,17 +86,12 @@ mito:
 The pipeline can be tested locally using a provided small test dataset:
 
 ```
-cd ${GENOMEASSEMBLY_TEST_DATA}
-curl https://tolit.cog.sanger.ac.uk/test-data/resources/genomeassembly/genomeassembly_test_data.tar.gz | tar xzf -
-
 git clone [email protected]:sanger-tol/genomeassembly.git
 cd genomeassembly/
-sed -i "s|/home/runner/work/genomeassembly/genomeassembly|${GENOMEASSEMBLY_TEST_DATA}|" assets/test_github.yaml
 nextflow run main.nf -profile test_github,singularity --outdir ${OUTDIR} {OTHER ARGUMENTS}
 ```
 
-These command line steps will download and decompress the test data first, then download the pipeline and modify YAML so that it matches dataset location in your file system.
-The last command line runs the test.
+These command line steps will download the pipeline and run the test.
 
 You should now be able to run the pipeline as you see fit.