move links and reference into info for now

_viash.yaml

@@ -1 +1,6 @@
+name: biobase
+description: |
+  A collection of bioinformatics tools for working with sequence data.
+license: MIT
+
 viash_version: 0.9.0-RC1

src/arriba/config.vsh.yaml

@@ -2,12 +2,13 @@ functionality:
   name: arriba
   description: Detect gene fusions from RNA-Seq data
   keywords: [Gene fusion, RNA-Seq]
-  links:
-    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
+  info:
+    links:
+      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
   license: MIT
   requirements:
     cpus: 1

src/bgzip/config.vsh.yaml

@@ -1,10 +1,11 @@
 functionality:
   name: bgzip
   description: Block compression/decompression utility
-  links:
-    homepage: https://www.htslib.org/
-    documentation: https://www.htslib.org/doc/bgzip.html
-    repository: https://github.com/samtools/htslib
+  info:
+    links:
+      homepage: https://www.htslib.org/
+      documentation: https://www.htslib.org/doc/bgzip.html
+      repository: https://github.com/samtools/htslib
   license: MIT
   requirements:
     commands: [ bgzip ]

src/busco/config.vsh.yaml

@@ -2,12 +2,13 @@ functionality:
   name: busco
   description: Assessment of genome assembly and annotation completeness with single copy orthologs
   keywords: [Genome assembly, quality control]
-  links:
-    homepage: https://busco.ezlab.org/
-    documentation: https://busco.ezlab.org/busco_userguide.html
-    repository: https://gitlab.com/ezlab/busco
-  reference:
-    doi: "10.1007/978-1-4939-9173-0_14"
+  info:
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    reference:
+      doi: "10.1007/978-1-4939-9173-0_14"
   license: MIT
   argument_groups:
     - name: Inputs

src/fastp/config.vsh.yaml

@@ -21,12 +21,13 @@ functionality:
       - support interleaved input
       - support ultra-fast FASTQ-level deduplication
   keywords: [RNA-Seq, Trimming, Quality control]
-  links:
-    repository: https://github.com/OpenGene/fastp
-    documentation: https://github.com/OpenGene/fastp/blob/master/README.md
-  reference:
-    doi: "10.1093/bioinformatics/bty560"
-  licence: MIT
+  info:
+    links:
+      repository: https://github.com/OpenGene/fastp
+      documentation: https://github.com/OpenGene/fastp/blob/master/README.md
+    reference:
+      doi: "10.1093/bioinformatics/bty560"
+  license: MIT
   argument_groups:
     - name: Inputs
       description: |

src/featurecounts/config.vsh.yaml

@@ -3,13 +3,14 @@ functionality:
   description: |
     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.
   keywords: ["Read counting", "Genomic features"]
-  links:
-    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 
+  info:
+    links:
+      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"
+  license: GPL-3.0 
   requirements:
     commands: [ featureCounts ]