Merge pull request #39 from nf-core/full_test

Added full test config file.

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:dev
+image: nfcore/gitpod:latest
 tasks:
   - name: Update Nextflow and setup pre-commit
     command: |

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1dev - [2023.12.15]
+
+### `Added`
+
+- Added config file for full test dataset
+
 ## v1.0.1dev - [2023.12.11]
 
 Crop overview is provided to Multiqc - now when create_training_subset is run, multiqc and customdumpsoftwareversions are also run.

conf/test_full.config

@@ -14,11 +14,8 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/samplesheets/samplesheet_full_test.csv'
 
-    // Genome references
-    genome = 'R64-1-1'
+    segmentation_method = "mesmer,cellpose"
+    cellpose_pretrained_model = "nuclei"
 }