Merge pull request #112 from Ambys-Medicines/dsl2

DSL2: updated modules
nf-core · Oct 8, 2021 · b2ddd36 · b2ddd36
2 parents 42894f2 + 540f805
commit b2ddd36
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Showing 18 changed files with 217 additions and 147 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,2 +1,10 @@
-files_unchanged:
-  - lib/NfcoreSchema.groovy
+lint:
+  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
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"