add paths in output directive in cellranger cout module (nf-core#5108)

* add paths in output directive

* update meta.yml

* add stub file generation

* also create fake files in new stub

* update stub snaps as new output channels are now emitted

modules/nf-core/cellranger/count/main.nf

@@ -9,8 +9,10 @@ process CELLRANGER_COUNT {
     path  reference
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("**/outs/**")                          , emit: outs
+    tuple val(meta), path("**/outs/filtered_feature_bc_matrix**"), emit: filtered
+    tuple val(meta), path("**/outs/raw_feature_bc_matrix**")     , emit: raw
+    path "versions.yml"                                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +34,11 @@ process CELLRANGER_COUNT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${prefix}/outs/"
+    mkdir -p "${prefix}/outs/filtered_feature_bc_matrix"
+    mkdir -p "${prefix}/outs/raw_feature_bc_matrix"
     echo "$prefix" > ${prefix}/outs/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/filtered_feature_bc_matrix/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/raw_feature_bc_matrix/fake_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/cellranger/count/meta.yml

@@ -40,6 +40,14 @@ output:
       type: file
       description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
       pattern: "${meta.id}/outs/*"
+  - filtered:
+      type: file
+      description: Files containing the filtered outputs of Cell Ranger.
+      pattern: "**/outs/filtered_feature_bc_matrix**"
+  - raw:
+      type: file
+      description: Files containing the raw outputs of Cell Ranger.
+      pattern: "**/outs/raw_feature_bc_matrix**"
   - versions:
       type: file
       description: File containing software version