diff --git a/conf/test.config b/conf/test.config index 7c27314..1170bf7 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,8 +23,11 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'samplesheet_qc_only.csv'// Genome references - genome = 'R64-1-1' + input = params.pipelines_testdata_base_path + 'deepmutscan/samplesheet/GID1A_test.csv' + fasta = params.pipelines_testdata_base_path + 'deepmutscan/testdata/GID1A.fasta' + reading_frame = 352-1383 + min_counts = 2 + mutagenesis_type = max_diff_to_wt + run_seqdepth = true + fitness = true } diff --git a/nextflow_schema.json b/nextflow_schema.json index 706dcb2..0e27687 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -50,7 +50,7 @@ "type": "integer", "description": "minimum counts for variant to be recognized. All variants below min_counts will be set to 0", "minimum": 1, - "default": 3 + "default": 10 }, "sliding_window_size": { "type": "integer", @@ -262,7 +262,7 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true }, "trace_report_suffix": { diff --git a/testdata/README.md b/testdata/README.md deleted file mode 100644 index 219ecf1..0000000 --- a/testdata/README.md +++ /dev/null @@ -1 +0,0 @@ -4 x 50k sequencing reads (small pilot test data set) diff --git a/testdata/input1_50k_1.fastq.gz b/testdata/input1_50k_1.fastq.gz deleted file mode 100644 index 62fed3d..0000000 Binary files a/testdata/input1_50k_1.fastq.gz and /dev/null differ diff --git a/testdata/input1_50k_2.fastq.gz b/testdata/input1_50k_2.fastq.gz deleted file mode 100644 index bd888d9..0000000 Binary files a/testdata/input1_50k_2.fastq.gz and /dev/null differ diff --git a/testdata/input2_50k_1.fastq.gz b/testdata/input2_50k_1.fastq.gz deleted file mode 100644 index a23bb31..0000000 Binary files a/testdata/input2_50k_1.fastq.gz and /dev/null differ diff --git a/testdata/input2_50k_2.fastq.gz b/testdata/input2_50k_2.fastq.gz deleted file mode 100644 index e4166c5..0000000 Binary files a/testdata/input2_50k_2.fastq.gz and /dev/null differ diff --git a/testdata/output1_50k_1.fastq.gz b/testdata/output1_50k_1.fastq.gz deleted file mode 100644 index bffa42e..0000000 Binary files a/testdata/output1_50k_1.fastq.gz and /dev/null differ diff --git a/testdata/output1_50k_2.fastq.gz b/testdata/output1_50k_2.fastq.gz deleted file mode 100644 index 60a7cc4..0000000 Binary files a/testdata/output1_50k_2.fastq.gz and /dev/null differ diff --git a/testdata/output2_50k_1.fastq.gz b/testdata/output2_50k_1.fastq.gz deleted file mode 100644 index 48aec2a..0000000 Binary files a/testdata/output2_50k_1.fastq.gz and /dev/null differ diff --git a/testdata/output2_50k_2.fastq.gz b/testdata/output2_50k_2.fastq.gz deleted file mode 100644 index ac23137..0000000 Binary files a/testdata/output2_50k_2.fastq.gz and /dev/null differ