modify file extensions

EBI-Metagenomics · Jan 28, 2025 · 200aad2 · 200aad2
1 parent 96d54f7
commit 200aad2
Show file tree

Hide file tree

Showing 5 changed files with 29 additions and 26 deletions.
diff --git a/modules/ebi-metagenomics/summarisegoslims/main.nf b/modules/ebi-metagenomics/summarisegoslims/main.nf
@@ -15,9 +15,9 @@ process SUMMARISEGOSLIMS {
     path go_banding
 
     output:
-    tuple val(meta), path("*_summary"), emit: go_summary
-    tuple val(meta), path("*_slim")   , emit: goslim_summary
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*_summary.csv"), emit: go_summary
+    tuple val(meta), path("*_slim.csv")   , emit: goslim_summary
+    path "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,6 +32,9 @@ process SUMMARISEGOSLIMS {
         -gaf ${gaf} \\
         -o ${prefix}_summary
 
+    mv ${prefix}_summary ${prefix}_summary.csv
+    mv ${prefix}_summary_slim ${prefix}_summary_slim.csv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mgnify-pipelines-toolkit: \$(get_mpt_version)
@@ -41,8 +44,8 @@ process SUMMARISEGOSLIMS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_summary
-    touch ${prefix}_summary_slim
+    touch ${prefix}_summary.csv
+    touch ${prefix}_summary_slim.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/ebi-metagenomics/summarisegoslims/meta.yml b/modules/ebi-metagenomics/summarisegoslims/meta.yml
@@ -50,20 +50,20 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*_summary":
+      - "*_summary.csv":
           type: file
           description: CSV file containing the counts for the different GO terms in the InterProScan output.
-          pattern: "*_summary"
+          pattern: "*_summary.csv"
   - goslim_summary:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*_slim":
+      - "*_slim.csv":
           type: file
           description: CSV file containing the counts for the different GO-Slim terms in the InterProScan output.
-          pattern: "*_slim"
+          pattern: "*_slim.csv"
   - versions:
       - "versions.yml":
           type: file

diff --git a/modules/ebi-metagenomics/summarisegoslims/tests/main.nf.test.snap b/modules/ebi-metagenomics/summarisegoslims/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,ddf9aa47da0a848795fffb56d9ac3c96"
+                        "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,ce50e0507a12ef0d70bd41b14926c5d5"
+                        "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5"
                     ]
                 ],
                 "2": [
@@ -29,7 +29,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,ddf9aa47da0a848795fffb56d9ac3c96"
+                        "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96"
                     ]
                 ],
                 "goslim_summary": [
@@ -38,7 +38,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,ce50e0507a12ef0d70bd41b14926c5d5"
+                        "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5"
                     ]
                 ],
                 "versions": [
@@ -50,7 +50,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T11:18:05.198568257"
+        "timestamp": "2025-01-28T22:32:00.22627889"
     },
     "summarisegoslims - stub": {
         "content": [
@@ -61,7 +61,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_summary.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -70,7 +70,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_summary_slim.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_summary.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "goslim_summary": [
@@ -91,7 +91,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_summary_slim.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -103,6 +103,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T11:18:11.207305173"
+        "timestamp": "2025-01-28T22:32:06.80636831"
     }
 }
diff --git a/subworkflows/ebi-metagenomics/goslim_swf/meta.yml b/subworkflows/ebi-metagenomics/goslim_swf/meta.yml
@@ -36,13 +36,13 @@ output:
       description: |
         Channel containing GO term counts
         Structure: [ val(meta), path(csv) ]
-      pattern: "*_summary"
+      pattern: "*_summary.csv"
   - goslim_summary:
       type: file
       description: |
         Channel containing GO-slim term counts
         Structure: [ val(meta), path(csv) ]
-      pattern: "*_slim"
+      pattern: "*_slim.csv"
   - versions:
       type: file
       description: |

diff --git a/subworkflows/ebi-metagenomics/goslim_swf/tests/main.nf.test.snap b/subworkflows/ebi-metagenomics/goslim_swf/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,ddf9aa47da0a848795fffb56d9ac3c96"
+                        "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,ce50e0507a12ef0d70bd41b14926c5d5"
+                        "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5"
                     ]
                 ],
                 "2": [
@@ -31,7 +31,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary:md5,ddf9aa47da0a848795fffb56d9ac3c96"
+                        "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96"
                     ]
                 ],
                 "goslim_summary": [
@@ -40,7 +40,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_summary_slim:md5,ce50e0507a12ef0d70bd41b14926c5d5"
+                        "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5"
                     ]
                 ],
                 "versions": [
@@ -54,6 +54,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T17:09:33.939130884"
+        "timestamp": "2025-01-28T22:32:17.095895573"
     }
 }