diff --git a/nf-test.config b/nf-test.config index 257946ae65..c60f901961 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,6 +1,6 @@ config { testsDir "." workDir ".nf-test" - configFile "nextflow.config" + configFile "conf/test.config" profile "test" } diff --git a/subworkflows/local/samplesheet_to_channel/main.nf b/subworkflows/local/samplesheet_to_channel/main.nf index b4a153b0eb..458651ee3a 100644 --- a/subworkflows/local/samplesheet_to_channel/main.nf +++ b/subworkflows/local/samplesheet_to_channel/main.nf @@ -1,10 +1,3 @@ -// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/subworkflows -// You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A subworkflow SHOULD import at least two modules - - workflow SAMPLESHEET_TO_CHANNEL{ take: diff --git a/subworkflows/local/samplesheet_to_channel/main.nf.test b/subworkflows/local/samplesheet_to_channel/main.nf.test index 3d0ceff009..49eeb2a132 100644 --- a/subworkflows/local/samplesheet_to_channel/main.nf.test +++ b/subworkflows/local/samplesheet_to_channel/main.nf.test @@ -17,8 +17,8 @@ nextflow_workflow { // define inputs of the workflow here. Example: input[0] = Channel.of([['patient':'test', 'sample':'test', 'sex':'XX', 'status':0, 'lane':'test_L1'], - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz'), - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz'), + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), [], [], [], [], [], [], []]) """ }