From 2ab116166a01e7defe255aea1c56a4e4b1c70b1f Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Thu, 7 Oct 2021 16:53:54 -0700
Subject: [PATCH 1/6] updated module git SHA keys

---
 modules.json | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/modules.json b/modules.json
index fec24384..beaad357 100644
--- a/modules.json
+++ b/modules.json
@@ -4,35 +4,35 @@
     "repos": {
         "nf-core/modules": {
             "cat/fastq": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "fastqc": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "multiqc": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/flagstat": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/idxstats": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/index": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/sort": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/stats": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "samtools/view": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             },
             "trimgalore": {
-                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
+                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
             }
         }
     }
-}
\ No newline at end of file
+}

From 7f4bf3871553358360edd784c2925402d3f3fe78 Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Thu, 7 Oct 2021 17:16:04 -0700
Subject: [PATCH 2/6] force reinstalled modules to update

---
 modules.json                                  | 22 ++++----
 modules/local/get_software_versions.nf        |  1 +
 modules/local/samplesheet_check.nf            |  1 +
 .../modules/samtools/flagstat/functions.nf    | 54 +++++++++++--------
 .../nf-core/modules/samtools/flagstat/main.nf | 10 ++--
 .../modules/samtools/flagstat/meta.yml        |  6 +--
 .../modules/samtools/idxstats/functions.nf    | 54 +++++++++++--------
 .../nf-core/modules/samtools/idxstats/main.nf | 10 ++--
 .../modules/samtools/idxstats/meta.yml        |  6 +--
 .../modules/samtools/index/functions.nf       | 54 +++++++++++--------
 .../nf-core/modules/samtools/index/main.nf    | 10 ++--
 .../nf-core/modules/samtools/index/meta.yml   |  6 +--
 .../modules/samtools/sort/functions.nf        | 54 +++++++++++--------
 modules/nf-core/modules/samtools/sort/main.nf | 10 ++--
 .../nf-core/modules/samtools/sort/meta.yml    |  6 +--
 .../modules/samtools/stats/functions.nf       | 54 +++++++++++--------
 .../nf-core/modules/samtools/stats/main.nf    | 10 ++--
 .../nf-core/modules/samtools/stats/meta.yml   |  6 +--
 18 files changed, 218 insertions(+), 156 deletions(-)

diff --git a/modules.json b/modules.json
index beaad357..fec24384 100644
--- a/modules.json
+++ b/modules.json
@@ -4,35 +4,35 @@
     "repos": {
         "nf-core/modules": {
             "cat/fastq": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "fastqc": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "multiqc": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/flagstat": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/idxstats": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/index": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/sort": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/stats": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "samtools/view": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
             "trimgalore": {
-                "git_sha": "f479d4fb8d634b5ac5bd1c879917dc285abc076d"
+                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
index 6297eaa8..e1bd764d 100644
--- a/modules/local/get_software_versions.nf
+++ b/modules/local/get_software_versions.nf
@@ -2,6 +2,7 @@
 include { saveFiles } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process GET_SOFTWARE_VERSIONS {
     label 'process_low'
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 8330038d..6b539886 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -2,6 +2,7 @@
 include { saveFiles } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMPLESHEET_CHECK {
     label 'process_low'
diff --git a/modules/nf-core/modules/samtools/flagstat/functions.nf b/modules/nf-core/modules/samtools/flagstat/functions.nf
index da9da093..85628ee0 100644
--- a/modules/nf-core/modules/samtools/flagstat/functions.nf
+++ b/modules/nf-core/modules/samtools/flagstat/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/nf-core/modules/samtools/flagstat/main.nf b/modules/nf-core/modules/samtools/flagstat/main.nf
index d4852c66..f9115c6b 100644
--- a/modules/nf-core/modules/samtools/flagstat/main.nf
+++ b/modules/nf-core/modules/samtools/flagstat/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,12 +23,14 @@ process SAMTOOLS_FLAGSTAT {
 
     output:
     tuple val(meta), path("*.flagstat"), emit: flagstat
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     samtools flagstat $bam > ${bam}.flagstat
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/samtools/flagstat/meta.yml b/modules/nf-core/modules/samtools/flagstat/meta.yml
index 8414bf54..d408cb76 100644
--- a/modules/nf-core/modules/samtools/flagstat/meta.yml
+++ b/modules/nf-core/modules/samtools/flagstat/meta.yml
@@ -40,9 +40,9 @@ output:
         type: file
         description: File containing samtools flagstat output
         pattern: "*.{flagstat}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+        description: File containing software versions
+        pattern: "versions.yml"
 authors:
     - "@drpatelh"
diff --git a/modules/nf-core/modules/samtools/idxstats/functions.nf b/modules/nf-core/modules/samtools/idxstats/functions.nf
index da9da093..85628ee0 100644
--- a/modules/nf-core/modules/samtools/idxstats/functions.nf
+++ b/modules/nf-core/modules/samtools/idxstats/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/nf-core/modules/samtools/idxstats/main.nf b/modules/nf-core/modules/samtools/idxstats/main.nf
index 14a07cfb..b005088a 100644
--- a/modules/nf-core/modules/samtools/idxstats/main.nf
+++ b/modules/nf-core/modules/samtools/idxstats/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,12 +23,14 @@ process SAMTOOLS_IDXSTATS {
 
     output:
     tuple val(meta), path("*.idxstats"), emit: idxstats
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     samtools idxstats $bam > ${bam}.idxstats
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/samtools/idxstats/meta.yml b/modules/nf-core/modules/samtools/idxstats/meta.yml
index 530d0772..f4cb613f 100644
--- a/modules/nf-core/modules/samtools/idxstats/meta.yml
+++ b/modules/nf-core/modules/samtools/idxstats/meta.yml
@@ -41,9 +41,9 @@ output:
         type: file
         description: File containing samtools idxstats output
         pattern: "*.{idxstats}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+        description: File containing software versions
+        pattern: "versions.yml"
 authors:
     - "@drpatelh"
diff --git a/modules/nf-core/modules/samtools/index/functions.nf b/modules/nf-core/modules/samtools/index/functions.nf
index da9da093..85628ee0 100644
--- a/modules/nf-core/modules/samtools/index/functions.nf
+++ b/modules/nf-core/modules/samtools/index/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/nf-core/modules/samtools/index/main.nf b/modules/nf-core/modules/samtools/index/main.nf
index e1966fb3..febbc11c 100644
--- a/modules/nf-core/modules/samtools/index/main.nf
+++ b/modules/nf-core/modules/samtools/index/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,12 +24,14 @@ process SAMTOOLS_INDEX {
     output:
     tuple val(meta), path("*.bai"), optional:true, emit: bai
     tuple val(meta), path("*.csi"), optional:true, emit: csi
-    path  "*.version.txt"         , emit: version
+    path  "versions.yml"          , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     samtools index $options.args $bam
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/samtools/index/meta.yml b/modules/nf-core/modules/samtools/index/meta.yml
index 5d076e3b..5f4dd3fb 100644
--- a/modules/nf-core/modules/samtools/index/meta.yml
+++ b/modules/nf-core/modules/samtools/index/meta.yml
@@ -38,10 +38,10 @@ output:
         type: file
         description: CSI index file
         pattern: "*.{csi}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+        description: File containing software versions
+        pattern: "versions.yml"
 authors:
     - "@drpatelh"
     - "@ewels"
diff --git a/modules/nf-core/modules/samtools/sort/functions.nf b/modules/nf-core/modules/samtools/sort/functions.nf
index da9da093..85628ee0 100644
--- a/modules/nf-core/modules/samtools/sort/functions.nf
+++ b/modules/nf-core/modules/samtools/sort/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/nf-core/modules/samtools/sort/main.nf b/modules/nf-core/modules/samtools/sort/main.nf
index 0a6b7048..b30f6f45 100644
--- a/modules/nf-core/modules/samtools/sort/main.nf
+++ b/modules/nf-core/modules/samtools/sort/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,13 +23,15 @@ process SAMTOOLS_SORT {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path  "*.version.txt"         , emit: version
+    path  "versions.yml"          , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/samtools/sort/meta.yml b/modules/nf-core/modules/samtools/sort/meta.yml
index 704e8c1f..cd47c86d 100644
--- a/modules/nf-core/modules/samtools/sort/meta.yml
+++ b/modules/nf-core/modules/samtools/sort/meta.yml
@@ -34,10 +34,10 @@ output:
         type: file
         description: Sorted BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+        description: File containing software versions
+        pattern: "versions.yml"
 authors:
     - "@drpatelh"
     - "@ewels"
diff --git a/modules/nf-core/modules/samtools/stats/functions.nf b/modules/nf-core/modules/samtools/stats/functions.nf
index da9da093..85628ee0 100644
--- a/modules/nf-core/modules/samtools/stats/functions.nf
+++ b/modules/nf-core/modules/samtools/stats/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/modules/samtools/stats/main.nf
index 8c72d725..6218dd2d 100644
--- a/modules/nf-core/modules/samtools/stats/main.nf
+++ b/modules/nf-core/modules/samtools/stats/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,12 +23,14 @@ process SAMTOOLS_STATS {
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
-    path  "*.version.txt"           , emit: version
+    path  "versions.yml"            , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     samtools stats $bam > ${bam}.stats
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/samtools/stats/meta.yml b/modules/nf-core/modules/samtools/stats/meta.yml
index b549ff5c..d75d73e2 100644
--- a/modules/nf-core/modules/samtools/stats/meta.yml
+++ b/modules/nf-core/modules/samtools/stats/meta.yml
@@ -39,9 +39,9 @@ output:
         type: file
         description: File containing samtools stats output
         pattern: "*.{stats}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+        description: File containing software versions
+        pattern: "versions.yml"
 authors:
     - "@drpatelh"

From 66cb3d8a1c38c1d58d7536ac23566d33c88b0eba Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Thu, 7 Oct 2021 17:17:54 -0700
Subject: [PATCH 3/6] fixed file formatting issue with .nf-core.yml

---
 .nf-core.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 27e3032a..b3adb635 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,5 @@
+lint:
+  - actions_awsfulltest: False
+  - pipeline_todos: False:
 files_unchanged:
   - lib/NfcoreSchema.groovy

From dc5ac2507c3837cf7afb55382a63a7d6d9bd484b Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Thu, 7 Oct 2021 17:18:16 -0700
Subject: [PATCH 4/6] fixed file formatting issue with .nf-core.yml

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index b3adb635..eb44ee6d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,5 @@
 lint:
   - actions_awsfulltest: False
-  - pipeline_todos: False:
+  - pipeline_todos: False
 files_unchanged:
   - lib/NfcoreSchema.groovy

From 453cf74b4750a70b2054c92ebf67c588f15bcdd0 Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Fri, 8 Oct 2021 06:23:46 -0700
Subject: [PATCH 5/6] overwriting changes to .nf-core.yml to harmonize with
 nf-core/rnaseq

---
 .nf-core.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index eb44ee6d..25f2b4c3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,14 @@
 lint:
   - actions_awsfulltest: False
   - pipeline_todos: False
+  files_unchanged:
+    - .markdownlint.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - lib/NfcoreTemplate.groovy
+    - assets/multiqc_config.yaml
+  files_exist:
+    - bin/scrape_software_versions.py
+    - modules/local/get_software_versions.nf
 files_unchanged:
   - lib/NfcoreSchema.groovy

From 540f8054aa11634411e3a9a000fccdb81b918c7e Mon Sep 17 00:00:00 2001
From: "Kevin L. Keys" <kkeys@ambys.com>
Date: Fri, 8 Oct 2021 06:26:58 -0700
Subject: [PATCH 6/6] previous commit failed? harmonizing .nf-core.yml with
 nf-core/rnaseq

---
 .nf-core.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 25f2b4c3..daf3ed01 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,4 @@
 lint:
-  - actions_awsfulltest: False
-  - pipeline_todos: False
   files_unchanged:
     - .markdownlint.yml
     - assets/email_template.html
@@ -10,5 +8,3 @@ lint:
   files_exist:
     - bin/scrape_software_versions.py
     - modules/local/get_software_versions.nf
-files_unchanged:
-  - lib/NfcoreSchema.groovy