diff --git a/tests/modules/universc/main.nf b/tests/modules/universc/main.nf index 7cfb2e9be51..1634bf315ae 100644 --- a/tests/modules/universc/main.nf +++ b/tests/modules/universc/main.nf @@ -2,14 +2,32 @@ nextflow.enable.dsl = 2 +include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf' +include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf' include { UNIVERSC } from '../../../modules/universc/main.nf' -workflow test_universc { +workflow test_universc_10x { - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + input = [ [ id:'test', single_end:true, strandedness:'forward', gem: '123', samples: ["test_10x"] ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true) + ] ] - UNIVERSC ( input ) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + reference_name = "homo_sapiens_chr22_reference" + + CELLRANGER_MKGTF ( gtf ) + + CELLRANGER_MKREF ( + fasta, + CELLRANGER_MKGTF.out.gtf, + reference_name + ) + + UNIVERSC ( + input + CELLRANGER_MKREF.out.reference + ) } diff --git a/tests/modules/universc/nextflow.config b/tests/modules/universc/nextflow.config index 50f50a7a357..52a72a7b9d0 100644 --- a/tests/modules/universc/nextflow.config +++ b/tests/modules/universc/nextflow.config @@ -1,5 +1,9 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: UNIVERSC { + ext.args = '--chemistry="SC3Pv3" --technology="10x"' + } -} \ No newline at end of file +} diff --git a/tests/modules/universc/test.yml b/tests/modules/universc/test.yml index 034fb4ff7e7..0ce755f559c 100644 --- a/tests/modules/universc/test.yml +++ b/tests/modules/universc/test.yml @@ -1,11 +1,28 @@ -## TODO nf-core: Please run the following command to build this file: +## nf-core: Please run the following command to build this file: # nf-core modules create-test-yml universc -- name: "universc" - command: nextflow run ./tests/modules/universc -entry test_universc -c ./tests/config/nextflow.config -c ./tests/modules/universc/nextflow.config +- name: universc test_universc_10x + command: nextflow run tests/modules/universc -entry test_universc_10x -c tests/config/nextflow.config tags: - "universc" - # + - demultiplex + - cell-ranger + - single-cell + - 10x + - scRNA-Seq + - umi + - alignment + - quant + - RNA counts + - UMI counts + - RNA quantification + - STAR files: + - path: output/main.nf + md5sum: 216fbfe8b2f51de6e720c12043f95717 + - path: output/nextflow.config + md5sum: a44614a3c6420d316d52ea711b7f1aa6 + - path: output/test.yml + md5sum: afd1f8cf262db16cb2c710438aafb74e - path: "output/universc/test.bam" md5sum: e667c7caad0bc4b7ac383fd023c654fc - path: output/universc/versions.yml