Fix version string for mbuffer in bwafastalign (#11984)

ramprasadn · peterpru · web-flow · commit d6379deecb79 · 2026-06-12T07:20:04.000Z
* initial commit

* update container

* update test bwafastalign_mem

* update test

* merge multiple output channels

* review suggestions

* Update main.nf

* use ext.args

* fix config

* update configs

* update test

* update bwameme

* Update main.nf

* remove "version" in mbuffer version string

* update meta

* remove "version" in mbuffer's version string

* remove "version" string in mbuffer's version for bwafastalign/index

---------

Co-authored-by: peterpru &lt;peter.pruisscher@scilifelab.se&gt;
diff --git a/modules/nf-core/bwafastalign/index/main.nf b/modules/nf-core/bwafastalign/index/main.nf
@@ -15,7 +15,7 @@ process BWAFASTALIGN_INDEX {
     tuple val("${task.process}"), val('bwafastalign'), val('1.0.0'), topic: versions, emit: versions_bwafastalign
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | sed '1!d;s/.* //'") , topic: versions, emit: versions_samtools
-    tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer //p'") , topic: versions, emit: versions_mbuffer
+    tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer version //p'") , topic: versions, emit: versions_mbuffer
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/bwafastalign/index/meta.yml b/modules/nf-core/bwafastalign/index/meta.yml
@@ -66,7 +66,7 @@ output:
       - mbuffer:
           type: string
           description: The name of the tool
-      - mbuffer --version 2>&1 | sed -n 's/mbuffer //p':
+      - mbuffer --version 2>&1 | sed -n 's/mbuffer version //p':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -97,7 +97,7 @@ topics:
       - mbuffer:
           type: string
           description: The name of the tool
-      - mbuffer --version 2>&1 | sed -n 's/mbuffer //p':
+      - mbuffer --version 2>&1 | sed -n 's/mbuffer version //p':
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/bwafastalign/index/tests/main.nf.test.snap b/modules/nf-core/bwafastalign/index/tests/main.nf.test.snap
@@ -37,7 +37,7 @@
                     [
                         "BWAFASTALIGN_INDEX",
                         "mbuffer",
-                        "version 20160228"
+                        "20160228"
                     ]
                 ],
                 "index": [
@@ -68,7 +68,7 @@
                     [
                         "BWAFASTALIGN_INDEX",
                         "mbuffer",
-                        "version 20160228"
+                        "20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -80,11 +80,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-06-12T09:01:04.51149493",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-06-08T12:26:53.94075"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "BWAFASTALIGN index": {
         "content": [
@@ -110,7 +110,7 @@
                     [
                         "BWAFASTALIGN_INDEX",
                         "mbuffer",
-                        "version 20160228"
+                        "20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -122,10 +122,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-06-12T09:00:56.338215387",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-06-08T12:26:41.54578"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }
diff --git a/modules/nf-core/bwafastalign/mem/main.nf b/modules/nf-core/bwafastalign/mem/main.nf
@@ -18,7 +18,7 @@ process BWAFASTALIGN_MEM {
     tuple val(meta), path("${prefix}.{csi,crai}")    , emit: index , optional: true
     tuple val("${task.process}"), val('bwafastalign'), val('1.0.0'), topic: versions, emit: versions_bwafastalign
     tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | sed '1!d;s/.* //'") , topic: versions, emit: versions_samtools
-    tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer //p'") , topic: versions, emit: versions_mbuffer
+    tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer version//p'") , topic: versions, emit: versions_mbuffer
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/bwafastalign/mem/meta.yml b/modules/nf-core/bwafastalign/mem/meta.yml
@@ -63,7 +63,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.{sam,bam,cram}":
+      - ${prefix}.{sam,bam,cram}:
           type: file
           description: Output alignment file (SAM, BAM, or CRAM)
           pattern: "*.{sam,bam,cram}"
@@ -74,7 +74,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.{csi,crai}":
+      - ${prefix}.{csi,crai}:
           type: file
           description: Index file for BAM (.csi) or CRAM (.crai) output
           pattern: "*.{csi,crai}"
@@ -106,7 +106,7 @@ output:
       - mbuffer:
           type: string
           description: The name of the tool
-      - mbuffer --version 2>&1 | sed -n 's/mbuffer //p':
+      - mbuffer --version 2>&1 | sed -n 's/mbuffer version//p':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -135,7 +135,7 @@ topics:
       - mbuffer:
           type: string
           description: The name of the tool
-      - mbuffer --version 2>&1 | sed -n 's/mbuffer //p':
+      - mbuffer --version 2>&1 | sed -n 's/mbuffer version//p':
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap b/modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap
@@ -15,7 +15,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -27,7 +27,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-11T15:15:59.311623833",
+        "timestamp": "2026-06-12T08:29:18.833924106",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -72,7 +72,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "index": [
@@ -104,7 +104,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -116,7 +116,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-11T15:40:28.793626766",
+        "timestamp": "2026-06-12T08:32:15.456124051",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -138,7 +138,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -150,7 +150,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-11T15:40:18.344456977",
+        "timestamp": "2026-06-12T08:32:05.037964846",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -172,7 +172,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -184,7 +184,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-11T15:10:31.399321129",
+        "timestamp": "2026-06-12T08:23:56.737918563",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -206,7 +206,7 @@
                     [
                         "BWAFASTALIGN_MEM",
                         "mbuffer",
-                        "version 20160228"
+                        " 20160228"
                     ]
                 ],
                 "versions_samtools": [
@@ -218,7 +218,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-11T15:34:49.432709311",
+        "timestamp": "2026-06-12T08:26:37.839861629",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@`
`37`	`37`	`[`
`38`	`38`	`"BWAFASTALIGN_INDEX",`
`39`	`39`	`"mbuffer",`
`40`		`- "version 20160228"`
	`40`	`+ "20160228"`
`41`	`41`	`]`
`42`	`42`	`],`
`43`	`43`	`"index": [`
`@@ -68,7 +68,7 @@`
`68`	`68`	`[`
`69`	`69`	`"BWAFASTALIGN_INDEX",`
`70`	`70`	`"mbuffer",`
`71`		`- "version 20160228"`
	`71`	`+ "20160228"`
`72`	`72`	`]`
`73`	`73`	`],`
`74`	`74`	`"versions_samtools": [`
`@@ -80,11 +80,11 @@`
`80`	`80`	`]`
`81`	`81`	`}`
`82`	`82`	`],`
	`83`	`+ "timestamp": "2026-06-12T09:01:04.51149493",`
`83`	`84`	`"meta": {`
`84`		`- "nf-test": "0.9.3",`
`85`		`- "nextflow": "25.04.0"`
`86`		`- },`
`87`		`- "timestamp": "2026-06-08T12:26:53.94075"`
	`85`	`+ "nf-test": "0.9.5",`
	`86`	`+ "nextflow": "25.10.4"`
	`87`	`+ }`
`88`	`88`	`},`
`89`	`89`	`"BWAFASTALIGN index": {`
`90`	`90`	`"content": [`
`@@ -110,7 +110,7 @@`
`110`	`110`	`[`
`111`	`111`	`"BWAFASTALIGN_INDEX",`
`112`	`112`	`"mbuffer",`
`113`		`- "version 20160228"`
	`113`	`+ "20160228"`
`114`	`114`	`]`
`115`	`115`	`],`
`116`	`116`	`"versions_samtools": [`
`@@ -122,10 +122,10 @@`
`122`	`122`	`]`
`123`	`123`	`}`
`124`	`124`	`],`
	`125`	`+ "timestamp": "2026-06-12T09:00:56.338215387",`
`125`	`126`	`"meta": {`
`126`		`- "nf-test": "0.9.3",`
`127`		`- "nextflow": "25.04.0"`
`128`		`- },`
`129`		`- "timestamp": "2026-06-08T12:26:41.54578"`
	`127`	`+ "nf-test": "0.9.5",`
	`128`	`+ "nextflow": "25.10.4"`
	`129`	`+ }`
`130`	`130`	`}`
`131`	`131`	`}`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@`
`15`	`15`	`[`
`16`	`16`	`"BWAFASTALIGN_MEM",`
`17`	`17`	`"mbuffer",`
`18`		`- "version 20160228"`
	`18`	`+ " 20160228"`
`19`	`19`	`]`
`20`	`20`	`],`
`21`	`21`	`"versions_samtools": [`
`@@ -27,7 +27,7 @@`
`27`	`27`	`]`
`28`	`28`	`}`
`29`	`29`	`],`
`30`		`- "timestamp": "2026-06-11T15:15:59.311623833",`
	`30`	`+ "timestamp": "2026-06-12T08:29:18.833924106",`
`31`	`31`	`"meta": {`
`32`	`32`	`"nf-test": "0.9.5",`
`33`	`33`	`"nextflow": "25.10.4"`
`@@ -72,7 +72,7 @@`
`72`	`72`	`[`
`73`	`73`	`"BWAFASTALIGN_MEM",`
`74`	`74`	`"mbuffer",`
`75`		`- "version 20160228"`
	`75`	`+ " 20160228"`
`76`	`76`	`]`
`77`	`77`	`],`
`78`	`78`	`"index": [`
`@@ -104,7 +104,7 @@`
`104`	`104`	`[`
`105`	`105`	`"BWAFASTALIGN_MEM",`
`106`	`106`	`"mbuffer",`
`107`		`- "version 20160228"`
	`107`	`+ " 20160228"`
`108`	`108`	`]`
`109`	`109`	`],`
`110`	`110`	`"versions_samtools": [`
`@@ -116,7 +116,7 @@`
`116`	`116`	`]`
`117`	`117`	`}`
`118`	`118`	`],`
`119`		`- "timestamp": "2026-06-11T15:40:28.793626766",`
	`119`	`+ "timestamp": "2026-06-12T08:32:15.456124051",`
`120`	`120`	`"meta": {`
`121`	`121`	`"nf-test": "0.9.5",`
`122`	`122`	`"nextflow": "25.10.4"`
`@@ -138,7 +138,7 @@`
`138`	`138`	`[`
`139`	`139`	`"BWAFASTALIGN_MEM",`
`140`	`140`	`"mbuffer",`
`141`		`- "version 20160228"`
	`141`	`+ " 20160228"`
`142`	`142`	`]`
`143`	`143`	`],`
`144`	`144`	`"versions_samtools": [`
`@@ -150,7 +150,7 @@`
`150`	`150`	`]`
`151`	`151`	`}`
`152`	`152`	`],`
`153`		`- "timestamp": "2026-06-11T15:40:18.344456977",`
	`153`	`+ "timestamp": "2026-06-12T08:32:05.037964846",`
`154`	`154`	`"meta": {`
`155`	`155`	`"nf-test": "0.9.5",`
`156`	`156`	`"nextflow": "25.10.4"`
`@@ -172,7 +172,7 @@`
`172`	`172`	`[`
`173`	`173`	`"BWAFASTALIGN_MEM",`
`174`	`174`	`"mbuffer",`
`175`		`- "version 20160228"`
	`175`	`+ " 20160228"`
`176`	`176`	`]`
`177`	`177`	`],`
`178`	`178`	`"versions_samtools": [`
`@@ -184,7 +184,7 @@`
`184`	`184`	`]`
`185`	`185`	`}`
`186`	`186`	`],`
`187`		`- "timestamp": "2026-06-11T15:10:31.399321129",`
	`187`	`+ "timestamp": "2026-06-12T08:23:56.737918563",`
`188`	`188`	`"meta": {`
`189`	`189`	`"nf-test": "0.9.5",`
`190`	`190`	`"nextflow": "25.10.4"`
`@@ -206,7 +206,7 @@`
`206`	`206`	`[`
`207`	`207`	`"BWAFASTALIGN_MEM",`
`208`	`208`	`"mbuffer",`
`209`		`- "version 20160228"`
	`209`	`+ " 20160228"`
`210`	`210`	`]`
`211`	`211`	`],`
`212`	`212`	`"versions_samtools": [`
`@@ -218,7 +218,7 @@`
`218`	`218`	`]`
`219`	`219`	`}`
`220`	`220`	`],`
`221`		`- "timestamp": "2026-06-11T15:34:49.432709311",`
	`221`	`+ "timestamp": "2026-06-12T08:26:37.839861629",`
`222`	`222`	`"meta": {`
`223`	`223`	`"nf-test": "0.9.5",`
`224`	`224`	`"nextflow": "25.10.4"`