update UniverSC module

  unit tests and documentation

Author: TomKellyGenetics

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
+    )
 }

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"'
+    }
 
-}
+}

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