new structure including all outputs in a single folder

modules/nf-core/gmmdemux/main.nf

@@ -16,28 +16,28 @@ process GMMDEMUX {
  path examine
 
  output:
- tuple val(meta), path("${meta.id}/barcodes.tsv.gz" ), emit: barcodes
- tuple val(meta), path("${meta.id}/*.mtx.gz" ), emit: matrix
- tuple val(meta), path("${meta.id}/features.tsv.gz" ), emit: features
- tuple val(meta), path("${meta.id}/classification_report_${meta.id}" ), emit: classification_report
- tuple val(meta), path("summary_report_${meta.id}.txt" ), emit: summary_report, optional: true
- path "versions.yml" , emit: versions
+ tuple val(meta), path("barcodes.tsv.gz" ), emit: barcodes
+ tuple val(meta), path("matrix.mtx.gz" ), emit: matrix
+ tuple val(meta), path("features.tsv.gz" ), emit: features
+ tuple val(meta), path("GMM_*.csv" ), emit: classification_report
+ tuple val(meta), path("GMM_*.config" ), emit: config_report
+ tuple val(meta), path("summary_report_*.txt" ), emit: summary_report, optional: true
+ path "versions.yml" , emit: versions
 
  when:
  task.ext.when == null || task.ext.when
 
  script:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
- def type_report = type_report ? "-f ${prefix}/classification_report_${prefix}" : "-s ${prefix}/classification_report_${prefix}"
  def skip = skip ? "--skip $skip" : ""
  def examine_cells = examine ? "--extract $examine" : ""
- def summary_rep = summary_report ? "-r summary_report_${prefix}" : ""
  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}" : ""
  """
  if [[ ${summary_report} == true ]]; then
  cat /dev/null > summary_report_${prefix}.txt
- echo "summary report file created"
  fi
 
  GMM-demux $args \\
@@ -54,14 +54,15 @@ process GMMDEMUX {
  """
 
  stub:
- def prefix = task.ext.prefix ?: "${meta.id}"
  def VERSION = '0.2.2.3'
+ def prefix = task.ext.prefix ?: "${meta.id}"
  """
- mkdir ${prefix}
- touch ${prefix}/barcodes.tsv.gz
- touch ${prefix}/features.tsv.gz
- touch ${prefix}/matrix.mtx.gz
- touch ${prefix}/classification_report_${prefix}
+
+ echo "" | gzip > barcodes.tsv.gz
+ echo "" | gzip > features.tsv.gz
+ echo "" | gzip > matrix.mtx.gz
+ touch GMM_full.config
+ touch GMM_full.csv
 
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":

modules/nf-core/gmmdemux/meta.yml

@@ -59,22 +59,27 @@ output:
  type: file
  description: |
  barcodes tsv file with removed cell-hashing-identifiable multiplets
- pattern: "test/*.tsv.gz"
+ pattern: "barcodes.tsv.gz"
  - matrix:
  type: file
  description: |
  matrix mtx.tsv file with removed cell-hashing-identifiable multiplets
- pattern: "test/*.tsv.gz"
+ pattern: "matrix.mtx.gz"
  - features:
  type: file
  description: |
  features tsv file with removed cell-hashing-identifiable multiplets
- pattern: "test/*.tsv.gz"
+ pattern: "features.tsv.gz"
  - classification_report:
  type: file
  description: |
  full or simplified classification report
- pattern: "test/*_report_*.txt"
+ pattern: "GMM_*.csv"
+ - config_report:
+ type: file
+ description: |
+ Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.
+ pattern: "GMM_*.csv"
  - summary_report:
  type: file
  description: |

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

@@ -71,9 +71,8 @@ nextflow_process {
  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 process.success },
+ { assert snapshot( process.out ).match() }
  )
  }
 

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

@@ -1,188 +1,91 @@
 {
- "Standard_Multiome - 10x mtx": {
+ "Standard_Multiome - 10x mtx - Stub": {
  "content": [
  {
  "0": [
  [
  {
- "id": "test",
- "single_end": true
+ "id": "test"
  },
- "barcodes.tsv.gz:md5,8ce05fd0599d95476158177deaa48543"
+ "barcodes.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
  "1": [
  [
  {
- "id": "test",
- "single_end": true
+ "id": "test"
  },
- "matrix.mtx.gz:md5,a203d4315dfae4ff939fe60dec9b9846"
+ "matrix.mtx.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
  "2": [
  [
  {
- "id": "test",
- "single_end": true
+ "id": "test"
  },
- "features.tsv.gz:md5,d7abe6b89142a9cf23d75a434d13a789"
+ "features.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
  "3": [
  [
  {
- "id": "test",
- "single_end": true
+ "id": "test"
  },
- [
- "GMM_full.config:md5,5d74af7b15c1cd4abaa4696be78631b2",
- "GMM_full.csv:md5,5b10400b4962e55c5daa4ea22394ff41"
- ]
+ "GMM_full.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
  ]
  ],
  "4": [
  [
  {
- "id": "test",
- "single_end": true
+ "id": "test"
  },
- "summary_report_test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "GMM_full.config:md5,d41d8cd98f00b204e9800998ecf8427e"
  ]
  ],
  "5": [
- "versions.yml:md5,da37b016c394b4e8cc16afb83e6f4941"
- ],
- "barcodes": [
- [
- {
- "id": "test",
- "single_end": true
- },
- "barcodes.tsv.gz:md5,8ce05fd0599d95476158177deaa48543"
- ]
- ],
- "classification_report": [
- [
- {
- "id": "test",
- "single_end": true
- },
- [
- "GMM_full.config:md5,5d74af7b15c1cd4abaa4696be78631b2",
- "GMM_full.csv:md5,5b10400b4962e55c5daa4ea22394ff41"
- ]
- ]
- ],
- "features": [
- [
- {
- "id": "test",
- "single_end": true
- },
- "features.tsv.gz:md5,d7abe6b89142a9cf23d75a434d13a789"
- ]
- ],
- "matrix": [
- [
- {
- "id": "test",
- "single_end": true
- },
- "matrix.mtx.gz:md5,a203d4315dfae4ff939fe60dec9b9846"
- ]
- ],
- "summary_report": [
- [
- {
- "id": "test",
- "single_end": true
- },
- "summary_report_test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
- ]
+
  ],
- "versions": [
+ "6": [
  "versions.yml:md5,da37b016c394b4e8cc16afb83e6f4941"
- ]
- }
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "24.04.2"
- },
- "timestamp": "2024-07-26T13:49:27.371578"
- },
- "Standard_Multiome - 10x mtx - Stub": {
- "content": [
- {
- "0": [
- [
- {
- "id": "test"
- },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/barcodes.tsv.gz"
- ]
  ],
- "1": [
- [
- {
- "id": "test"
- },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/matrix.mtx.gz"
- ]
- ],
- "2": [
- [
- {
- "id": "test"
- },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/features.tsv.gz"
- ]
- ],
- "3": [
+ "barcodes": [
  [
  {
  "id": "test"
  },
- "classification_report_test:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "barcodes.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
- "4": [
-
- ],
- "5": [
- "versions.yml:md5,da37b016c394b4e8cc16afb83e6f4941"
- ],
- "barcodes": [
+ "classification_report": [
  [
  {
  "id": "test"
  },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/barcodes.tsv.gz"
+ "GMM_full.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
  ]
  ],
- "classification_report": [
+ "config_report": [
  [
  {
  "id": "test"
  },
- "classification_report_test:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "GMM_full.config:md5,d41d8cd98f00b204e9800998ecf8427e"
  ]
  ],
  "features": [
  [
  {
  "id": "test"
  },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/features.tsv.gz"
+ "features.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
  "matrix": [
  [
  {
  "id": "test"
  },
- "/Users/mylenemarianagonzalesandre/Development/HiWi/nf-core/gmm-demux/modules/.nf-test/tests/7eb233d1843e36f276a6f58572e05321/work/43/54cffeebab21850b5b74ec9d5aab4b/test/matrix.mtx.gz"
+ "matrix.mtx.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
  ]
  ],
  "summary_report": [
@@ -197,6 +100,6 @@
  "nf-test": "0.8.4",
  "nextflow": "24.04.3"
  },
- "timestamp": "2024-07-29T14:41:14.557411"
+ "timestamp": "2024-07-30T15:00:17.240999"
  }
 }

modules/nf-core/gmmdemux/tests/nextflow.config

@@ -4,12 +4,14 @@ params{
  num_cells = 35685
  examine = "example_cell_types.txt"
  ambiguous = 0.05
- output_path = 'test'
+
 
 }
 
 process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
  withName: GMMDEMUX {
- ext.args = "-t ${params.threshold} --summary ${params.num_cells} -o ${params.output_path} -a ${params.ambiguous} "
+ ext.args = "-t ${params.threshold} -o . --summary ${params.num_cells} -a ${params.ambiguous} "
  }
 }