From 0366857f2c6aa5908b6e152f94c8712a4b2bbe01 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 31 Jan 2024 13:40:49 +0100
Subject: [PATCH] move links and reference into info for now

---
 _viash.yaml                       |  5 +++++
 src/arriba/config.vsh.yaml        | 13 +++++++------
 src/bgzip/config.vsh.yaml         |  9 +++++----
 src/busco/config.vsh.yaml         | 13 +++++++------
 src/fastp/config.vsh.yaml         | 13 +++++++------
 src/featurecounts/config.vsh.yaml | 15 ++++++++-------
 6 files changed, 39 insertions(+), 29 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index b4133db8..7b5386d2 100644
--- a/_viash.yaml
+++ b/_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
\ No newline at end of file
diff --git a/src/arriba/config.vsh.yaml b/src/arriba/config.vsh.yaml
index 2439af57..1f9c78a9 100644
--- a/src/arriba/config.vsh.yaml
+++ b/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
diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml
index 95f2d6a1..7525328e 100644
--- a/src/bgzip/config.vsh.yaml
+++ b/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 ]
diff --git a/src/busco/config.vsh.yaml b/src/busco/config.vsh.yaml
index d1686c3f..fdebb0f0 100644
--- a/src/busco/config.vsh.yaml
+++ b/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
diff --git a/src/fastp/config.vsh.yaml b/src/fastp/config.vsh.yaml
index 3ccef8cd..3fe04869 100644
--- a/src/fastp/config.vsh.yaml
+++ b/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: |
diff --git a/src/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml
index d9b2442c..1a4af4f2 100644
--- a/src/featurecounts/config.vsh.yaml
+++ b/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 ]