added simple test, fix for argument

modules/nf-core/gmmdemux/main.nf

@@ -31,13 +31,13 @@ process GMMDEMUX {
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def skip = skip ? "--skip $skip" : ""
- def examine_cells = examine ? "--extract $examine" : ""
+ def examine_cells = examine ? "--examine $examine" : ""
  def VERSION = '0.2.2.3' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
  def type_report = type_report ? "-f ." : "-s ."
- def summary_rep = summary_report ? "-r summary_report_${prefix}" : ""
+ def summary_rep = summary_report ? "-r ${prefix}_summary_report.txt" : ""
  """
  if [[ ${summary_report} == true ]]; then
- cat /dev/null > summary_report_${prefix}.txt
+ cat /dev/null > ${prefix}_summary_report.txt
  fi
 
  GMM-demux $args \\

modules/nf-core/gmmdemux/tests/main.nf.test

@@ -4,16 +4,50 @@ nextflow_process {
  name "Test Process GMMDEMUX"
  script "../main.nf"
  process "GMMDEMUX"
- config "./nextflow.config"
 
  tag "modules"
  tag "modules_nfcore"
  tag "gmmdemux"
  tag "untar"
 
 
+ test("Standard_Multiome - 10x mtx - simple") {
+ setup {
+ run("UNTAR") {
+ script "modules/nf-core/untar/main.nf"
+ process {
+ """
+ input[0] = Channel.of([ [],file(params.modules_testdata_base_path + "/genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/hto.tar.gz", checkIfExists: true) ]) 
+ """
+ }
+ } 
+ }
+ when {
+ process {
+ """
+ input[0] = UNTAR.out.untar.map { meta, files -> [ [ id:'test', single_end:true ], files, "MS-11,MS-12" ] }
+ input[1] = false
+ input[2] = false
+ input[3] = []
+ input[4] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.matrix.get(0).get(1)).exists() },
+ { assert path(process.out.barcodes.get(0).get(1)).exists() },
+ { assert path(process.out.features.get(0).get(1)).exists() },
+ { assert path(process.out.config_report.get(0).get(1)).exists() },
+
+ )
+ }
+ }
 
  test("Standard_Multiome - 10x mtx") {
+ config "./nextflow.config"
  setup {
  run("UNTAR") {
  script "modules/nf-core/untar/main.nf"
@@ -49,7 +83,7 @@ nextflow_process {
  }
 
  test("Standard_Multiome - 10x mtx - stub") {
-
+ config "./nextflow.config"
  options "-stub"
 
  when {