From e437bb6ecfbf1e78d6dec91495c92c45a9588fe4 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Fri, 15 Dec 2023 13:53:54 +0000 Subject: [PATCH 1/4] Added full test config file. --- conf/test_full.config | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index e0e4cef..dae9919 100644 --- a/conf/test_full.config +++ b/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" } From 5b53fb3454a65a059ae1c9c653a3e9060b02ca22 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Fri, 15 Dec 2023 13:58:26 +0000 Subject: [PATCH 2/4] Updated changelog. --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a3e7f6a..098a749 100644 --- a/CHANGELOG.md +++ b/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. From f4c22fe8b75434cc8d12b156a45ee3b3f5c25f72 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Sat, 16 Dec 2023 10:02:27 +0000 Subject: [PATCH 3/4] Fixed formatting. --- conf/test_full.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index dae9919..a911dc3 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,6 +16,6 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/samplesheets/samplesheet_full_test.csv' - segmentation_method = "mesmer,cellpose" - cellpose_pretrained_model: "nuclei" + segmentation_method = "mesmer,cellpose" + cellpose_pretrained_model = "nuclei" } From 3b654a34e21746ab4cf9a180287d8861f174582a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= Date: Sat, 16 Dec 2023 10:27:34 +0000 Subject: [PATCH 4/4] reverted nfcore gitpod to latest --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index f9d9c8b..25488dc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:dev +image: nfcore/gitpod:latest tasks: - name: Update Nextflow and setup pre-commit command: |