From 714f665293359015fb758a1426a86463c1c90e98 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <almeidafmarques@gmail.com>
Date: Wed, 20 Mar 2024 11:19:46 +0100
Subject: [PATCH] Revert "add paths in output directive in cellranger cout
 module" (#5306)

Revert "add paths in output directive in cellranger cout module (#5108)"

This reverts commit 92ca535c5a8c0fe89eb71e649ee536bd355ce4fc.
---
 modules/nf-core/cellranger/count/main.nf      | 10 +---
 modules/nf-core/cellranger/count/meta.yml     |  8 ---
 .../cellranger/count/tests/main.nf.test.snap  | 52 +------------------
 3 files changed, 4 insertions(+), 66 deletions(-)

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 1811d7457ff..42aa09c9f5b 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -9,10 +9,8 @@ process CELLRANGER_COUNT {
     path  reference
 
     output:
-    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
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,11 +32,7 @@ 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
     "${task.process}":
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
index 562449769b8..1f1768a857b 100644
--- a/modules/nf-core/cellranger/count/meta.yml
+++ b/modules/nf-core/cellranger/count/meta.yml
@@ -40,14 +40,6 @@ output:
       type: file
       description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
       pattern: "${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
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
index edfb304b733..7eafafd02e9 100644
--- a/modules/nf-core/cellranger/count/tests/main.nf.test.snap
+++ b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
@@ -27,30 +27,6 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test_10x",
-                            "single_end": false,
-                            "strandedness": "auto"
-                        },
-                        [
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_10x",
-                            "single_end": false,
-                            "strandedness": "auto"
-                        },
-                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
-                    ]
-                ],
-                "2": [
                     [
                         {
                             "id": "test_10x",
@@ -60,34 +36,10 @@
                         "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
                     ]
                 ],
-                "3": [
+                "1": [
                     "versions.yml:md5,30cee1a9146b01c48d9b1db6bbe813b6"
                 ],
-                "filtered": [
-                    [
-                        {
-                            "id": "test_10x",
-                            "single_end": false,
-                            "strandedness": "auto"
-                        },
-                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
-                    ]
-                ],
                 "outs": [
-                    [
-                        {
-                            "id": "test_10x",
-                            "single_end": false,
-                            "strandedness": "auto"
-                        },
-                        [
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
-                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
-                        ]
-                    ]
-                ],
-                "raw": [
                     [
                         {
                             "id": "test_10x",
@@ -106,6 +58,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T11:41:17.258523741"
+        "timestamp": "2024-03-05T17:16:12.322822411"
     }
 }
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