diff --git a/assets/samplesheet.json b/assets/samplesheet.json new file mode 100644 index 0000000..eb0e68c --- /dev/null +++ b/assets/samplesheet.json @@ -0,0 +1,16 @@ +[ + { + "sample": "SAMPLE1", + "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz", + "fastq_2": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz" + }, + { + "sample": "SAMPLE2", + "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz", + "fastq_2": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz" + }, + { + "sample": "SAMPLE3", + "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz" + } +] diff --git a/nextflow_schema.json b/nextflow_schema.json index f596d1e..2d301f8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -17,7 +17,7 @@ "format": "file-path", "exists": true, "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", + "pattern": "^\\S+\\.(csv|json)$", "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.", diff --git a/tests/default.nf.test b/tests/default.nf.test index 9da3d20..355b483 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -7,6 +7,7 @@ nextflow_pipeline { test("-profile test") { when { params { + input = "${projectDir}/assets/samplesheet.json" outdir = "$outputDir" } }