fix missing quotes

modules/nf-core/bamstats/generalstats/meta.yml

@@ -45,9 +45,10 @@ output:
       - bamstats:
           type: string
           description: The name of the tool
-      - 'bamstats --version | grep "version: " | sed -e s"/version: //':
-          type: string
-          description: The version of the tool
+      - 'bamstats --version | grep "version: " | sed -e s"/version: //"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -56,8 +57,9 @@ topics:
       - bamstats:
           type: string
           description: The name of the tool
-      - 'bamstats --version | grep "version: " | sed -e s"/version: //':
+      - 'bamstats --version | grep "version: " | sed -e s"/version: //"':
           type: eval
           description: The expression to obtain the version of the tool
+
 authors:
   - "@johnoooh"

modules/nf-core/bedgovcf/meta.yml

@@ -71,9 +71,10 @@ output:
       - bgzip:
           type: string
           description: The tool name
-      - bgzip --version | head -1 | sed "s/bgzip (htslib:
+      - bgzip --version | head -1 | sed "s/bgzip (htslib) //":
           type: eval
-          description: The tool version
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -91,8 +92,9 @@ topics:
       - bgzip:
           type: string
           description: The tool name
-      - bgzip --version | head -1 | sed "s/bgzip (htslib:
+      - bgzip --version | head -1 | sed "s/bgzip (htslib) //":
           type: eval
-          description: The tool version
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@nvnieuwk"

modules/nf-core/fastqc/meta.yml

@@ -60,9 +60,10 @@ output:
       - fastqc:
           type: string
           description: The tool name
-      - fastqc --version | sed "/FastQC v/!d; s/.*v//:
-          type: string
-          description: The command used to generate the version of the tool
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -71,9 +72,10 @@ topics:
       - fastqc:
           type: string
           description: The tool name
-      - fastqc --version | sed "/FastQC v/!d; s/.*v//:
-          type: string
-          description: The command used to generate the version of the tool
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@grst"

modules/nf-core/haplogrep3/classify/meta.yml

@@ -42,9 +42,10 @@ output:
       - haplogrep3:
           type: string
           description: The tool name
-      - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\':
-          type: string
-          description: The command used to generate the version of the tool
+      - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -53,9 +54,10 @@ topics:
       - haplogrep3:
           type: string
           description: The tool name
-      - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\':
-          type: string
-          description: The command used to generate the version of the tool
+      - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@lucpen"
 maintainers:

modules/nf-core/multiqc/meta.yml

@@ -80,9 +80,10 @@ output:
       - multiqc:
           type: string
           description: The tool name
-      - multiqc --version | sed "s/.* //g:
-          type: string
-          description: The command used to generate the version of the tool
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -91,9 +92,10 @@ topics:
       - multiqc:
           type: string
           description: The tool name
-      - multiqc --version | sed "s/.* //g:
-          type: string
-          description: The command used to generate the version of the tool
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@abhi18av"
   - "@bunop"

modules/nf-core/qsv/cat/meta.yml

@@ -31,11 +31,13 @@ input:
       pattern: "^(rows|columns|rowskey)$"
   - out_format:
       type: string
-      description: Output format (.csv for comma delimiter, .ssv for semicolon, and .tsv or .tab for tab)
+      description: Output format (.csv for comma delimiter, .ssv for semicolon,
+        and .tsv or .tab for tab)
       pattern: "^(csv|ssv|tsv|tab)$"
   - skip_input_format_check:
       type: boolean
-      description: Skip input format check (by default QSV checks input format based on file extension)
+      description: Skip input format check (by default QSV checks input format
+        based on file extension)
 output:
   csv:
     - - meta:
@@ -50,7 +52,7 @@ output:
           ontologies:
             - edam: http://edamontology.org/format_3752 # CSV
             - edam: http://edamontology.org/format_3475 # TSV
-  versions_qsv: &versions
+  versions_qsv:
     - - ${task.process}:
           type: string
           description: The name of the process
@@ -61,7 +63,16 @@ output:
           type: eval
           description: The expression to obtain the version of the tool
 topics:
-  versions: *versions
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - qsv:
+          type: string
+          description: The name of the tool
+      - "qsv --version | cut -d' ' -f2 | cut -d'-' -f1":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@dialvarezs"
 maintainers:

modules/nf-core/ribodetector/meta.yml

@@ -1,6 +1,6 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "ribodetector"
-description: Accurate and rapid RiboRNA sequences Detector based on deep learning
+description: Accurate and rapid RiboRNA sequences Detector based on deep
+  learning
 keywords:
   - RNA
   - RNAseq
@@ -14,12 +14,12 @@ keywords:
   - genomics
 tools:
   - ribodetector:
-      description: Accurate and rapid RiboRNA sequences detector based on deep learning.
-        RiboDetector uses a deep learning approach to identify rRNA sequences in ribosome
-        profiling (Ribo-seq) data. It can be used to filter out rRNA reads from Ribo-seq
-        datasets, improving the quality of downstream analyses. As of version 0.3.1,
-        Ribodetector doesn't support setting a random seed, so results may not be fully
-        deterministic across runs.
+      description: Accurate and rapid RiboRNA sequences detector based on deep
+        learning. RiboDetector uses a deep learning approach to identify rRNA
+        sequences in ribosome profiling (Ribo-seq) data. It can be used to filter
+        out rRNA reads from Ribo-seq datasets, improving the quality of downstream
+        analyses. As of version 0.3.1, Ribodetector doesn't support setting a
+        random seed, so results may not be fully deterministic across runs.
       homepage: "https://github.com/hzi-bifo/RiboDetector"
       documentation: "https://github.com/hzi-bifo/RiboDetector"
       tool_dev_url: "https://github.com/hzi-bifo/RiboDetector"
@@ -73,9 +73,10 @@ output:
       - ribodetector:
           type: string
           description: Name of the tool
-      - ribodetector --version | sed "s/ribodetector //:
-          type: string
-          description: Version of ribodetector used
+      - ribodetector --version | sed "s/ribodetector //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -84,9 +85,10 @@ topics:
       - ribodetector:
           type: string
           description: Name of the tool
-      - ribodetector --version | sed "s/ribodetector //:
-          type: string
-          description: Version of ribodetector used
+      - ribodetector --version | sed "s/ribodetector //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@maxibor"
 maintainers:

modules/nf-core/samtools/sort/meta.yml

@@ -131,6 +131,7 @@ topics:
       - "samtools version | sed '1!d;s/.* //'":
           type: string
           description: The command used to generate the version of the tool
+
 authors:
   - "@drpatelh"
   - "@ewels"

modules/nf-core/samtools/stats/meta.yml

@@ -62,21 +62,22 @@ output:
       - samtools:
           type: string
           description: Name of the tool
-      - samtools version | sed "1!d;s/.* //:
-          type: string
-          description: The command used to generate the version of the tool
+      - samtools version | sed "1!d;s/.* //":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 topics:
   versions:
     - - ${task.process}:
           type: string
-          description: The process the versions were collected from
+          description: Name of the process
       - samtools:
           type: string
-          description: The tool name
-      - samtools version | sed "1!d;s/.* //:
-          type: string
-          description: The command used to generate the version of the tool
+          description: Name of the tool
+      - samtools version | sed "1!d;s/.* //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@FriederikeHanssen"

modules/nf-core/samtools/view/meta.yml

@@ -147,9 +147,10 @@ output:
       - samtools:
           type: string
           description: Name of the tool
-      - samtools --version | head -1 | sed -e "s/samtools //:
-          type: string
-          description: Version of samtools used
+      - samtools --version | head -1 | sed -e "s/samtools //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -158,9 +159,10 @@ topics:
       - samtools:
           type: string
           description: Name of the tool
-      - samtools --version | head -1 | sed -e "s/samtools //:
-          type: string
-          description: Version of samtools used
+      - samtools --version | head -1 | sed -e "s/samtools //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@joseespinosa"

modules/nf-core/semibin/singleeasybin/meta.yml

@@ -76,7 +76,7 @@ output:
           description: precluster fasta files
           pattern: "*.fa"
           ontologies: []
-  versions_semibin: &versions
+  versions_semibin:
     - - ${task.process}:
           type: string
           description: The name of the process
@@ -87,7 +87,16 @@ output:
           type: eval
           description: The expression to obtain the version of the tool
 topics:
-  versions: *versions
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - SemiBin:
+          type: string
+          description: The name of the tool
+      - "SemiBin2 --version":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@BigDataBiology"
 maintainers:

modules/nf-core/strdrop/build/meta.yml

@@ -62,6 +62,7 @@ topics:
       - strdrop --version | sed 's/.* //g':
           type: eval
           description: The expression to obtain the version of the tool
+
 authors:
   - "@fellen31"
 maintainers:

modules/nf-core/tabix/tabix/meta.yml

@@ -36,26 +36,28 @@ output:
           pattern: "*.{tbi,csi}"
           ontologies: []
   versions_tabix:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The process the versions were collected from
-      - "tabix":
+      - tabix:
           type: string
           description: The tool name
-      - tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+':
-          type: string
-          description: The command used to generate the version of the tool
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 topics:
   versions:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The process the versions were collected from
-      - "tabix":
+      - tabix:
           type: string
           description: The tool name
-      - tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+':
-          type: string
-          description: The command used to generate the version of the tool
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"