uniformize metadata

src/arriba/config.vsh.yaml

@@ -3,11 +3,13 @@ functionality:
   description: Detect gene fusions from RNA-Seq data
   info:
     keywords: [Gene fusion, RNA-Seq]
-    homepage: https://arriba.readthedocs.io/en/latest/
-    documentation: https://arriba.readthedocs.io/en/latest/
-    repository: https://github.com/suhrig/arriba
-    reference: "doi:10.1101/gr.257246.119"
-    licence: MIT
+    links:
+      homepage: https://arriba.readthedocs.io/en/latest/
+      documentation: https://arriba.readthedocs.io/en/latest/
+      repository: https://github.com/suhrig/arriba
+    references:
+      doi: 10.1101/gr.257246.119
+    license: MIT
   requirements:
     cpus: 1
     commands: [ arriba ]

src/bgzip/config.vsh.yaml

@@ -2,12 +2,13 @@ functionality:
   name: bgzip
   description: Block compression/decompression utility
   info:
-    homepage: https://www.htslib.org/
-    documentation: https://www.htslib.org/doc/bgzip.html
-    repository: https://github.com/samtools/htslib
-    licence: MIT
-    reference:
+    links:
+      homepage: https://www.htslib.org/
+      documentation: https://www.htslib.org/doc/bgzip.html
+      repository: https://github.com/samtools/htslib
+    references:
       doi: 10.1093/gigascience/giab007
+    license: MIT
   requirements:
     commands: [ bgzip ]
   argument_groups:

src/busco/busco_download_datasets/config.vsh.yaml

@@ -4,11 +4,13 @@ functionality:
   description: Downloads available busco datasets
   info:
     keywords: [lineage datasets]
-    homepage: https://busco.ezlab.org/
-    documentation: https://busco.ezlab.org/busco_userguide.html
-    repository: https://gitlab.com/ezlab/busco
-    reference: "10.1007/978-1-4939-9173-0_14"
-    licence: MIT
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
   argument_groups:
     - name: Inputs
       arguments:

src/busco/busco_list_datasets/config.vsh.yaml

@@ -4,11 +4,13 @@ functionality:
   description: Lists the available busco datasets
   info:
     keywords: [lineage datasets]
-    homepage: https://busco.ezlab.org/
-    documentation: https://busco.ezlab.org/busco_userguide.html
-    repository: https://gitlab.com/ezlab/busco
-    reference: "10.1007/978-1-4939-9173-0_14"
-    licence: MIT
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
   argument_groups:
     - name: Outputs
       arguments:

src/busco/busco_run/config.vsh.yaml

@@ -4,11 +4,13 @@ functionality:
   description: Assessment of genome assembly and annotation completeness with single copy orthologs
   info:
     keywords: [Genome assembly, quality control]
-    homepage: https://busco.ezlab.org/
-    documentation: https://busco.ezlab.org/busco_userguide.html
-    repository: https://gitlab.com/ezlab/busco
-    reference: "10.1007/978-1-4939-9173-0_14"
-    licence: MIT
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
   argument_groups:
     - name: Inputs
       arguments:

src/fastp/config.vsh.yaml

@@ -22,10 +22,12 @@ functionality:
       - support ultra-fast FASTQ-level deduplication
   info:
     keywords: [RNA-Seq, Trimming, Quality control]
-    repository: https://github.com/OpenGene/fastp
-    documentation: https://github.com/OpenGene/fastp/blob/master/README.md
-    reference: "doi:10.1093/bioinformatics/bty560"
-    licence: MIT
+    links:
+      repository: https://github.com/OpenGene/fastp
+      documentation: https://github.com/OpenGene/fastp/blob/master/README.md
+    references:
+      doi: 10.1093/bioinformatics/bty560
+    license: MIT
   argument_groups:
     - name: Inputs
       description: |

src/featurecounts/config.vsh.yaml

@@ -4,11 +4,13 @@ functionality:
     featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.
   info:
     keywords: ["Read counting", "Genomic features"]
-    homepage: https://subread.sourceforge.net/
-    documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
-    repository: https://github.com/ShiLab-Bioinformatics/subread
-    reference: "doi:10.1093/bioinformatics/btt656"
-    licence: GPL-3.0 
+    links:
+      homepage: https://subread.sourceforge.net/
+      documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
+      repository: https://github.com/ShiLab-Bioinformatics/subread
+    references:
+      doi: 10.1093/bioinformatics/btt656
+    license: GPL-3.0 
   requirements:
     commands: [ featureCounts ]
 

src/pear/config.vsh.yaml

@@ -6,11 +6,13 @@ functionality:
     PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.
   info:
     keywords: [ "pair-end", "read", "merge" ]
-    homepage: https://cme.h-its.org/exelixis/web/software/pear
-    repository: https://github.com/tseemann/PEAR
-    documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html
-    reference: doi:10.1093/bioinformatics/btt593
-    licence: "CC-BY-NC-SA-3.0"
+    links:
+      homepage: https://cme.h-its.org/exelixis/web/software/pear
+      repository: https://github.com/tseemann/PEAR
+      documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html
+    references:
+      doi: 10.1093/bioinformatics/btt593
+    license: "CC-BY-NC-SA-3.0"
   requirements:
     commands: [ pear , gzip ]
   argument_groups: