Merge pull request #28 from CCBR/samtools-sort-index

fix: emit bai file from samtools/sort
CCBR · Oct 24, 2023 · bceab20 · bceab20
2 parents e838c93 + d55ab25
commit bceab20
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,7 @@
 - khmer/uniquekmers (#7)
 - picard/samtofastq (#21)
 - samtools/filteraligned (#13,#20)
-- samtools/sort (#24)
+- samtools/sort (#24,#28)
 
 ### New subworkflows
 

diff --git a/modules/CCBR/samtools/sort/main.nf b/modules/CCBR/samtools/sort/main.nf
@@ -8,9 +8,9 @@ process SAMTOOLS_SORT {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.csi"), emit: csi, optional: true
-    path("versions.yml")          , emit: versions
+    tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
+    tuple val(meta), path("*.csi"),                emit: csi, optional: true
+    path("versions.yml"),                          emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/CCBR/samtools/sort/tests/main.nf.test.snap b/modules/CCBR/samtools/sort/tests/main.nf.test.snap
@@ -8,7 +8,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716"
+                        "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716",
+                        "test.sorted.bam.bai:md5,be2757b9479e364588d855a77a251940"
                     ]
                 ],
                 "1": [
@@ -23,7 +24,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716"
+                        "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716",
+                        "test.sorted.bam.bai:md5,be2757b9479e364588d855a77a251940"
                     ]
                 ],
                 "csi": [
@@ -34,7 +36,7 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-24T12:35:29.864751"
+        "timestamp": "2023-10-24T13:53:20.473892"
     },
     "test_samtools_sort_stub": {
         "content": [
@@ -45,7 +47,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -60,7 +63,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "csi": [
@@ -71,6 +75,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-24T12:32:18.504111"
+        "timestamp": "2023-10-24T13:53:25.129302"
     }
 }