update to viash 0.9.0-RC1

_viash.yaml

@@ -1 +1 @@
-viash_version: 0.8.4
+viash_version: 0.9.0-RC1

src/arriba/config.vsh.yaml

@@ -1,13 +1,14 @@
 functionality:
   name: arriba
   description: Detect gene fusions from RNA-Seq data
-  info:
-    keywords: [Gene fusion, RNA-Seq]
+  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"
-    licence: MIT
+  reference:
+    doi: 10.1101/gr.257246.119
+  license: MIT
   requirements:
     cpus: 1
     commands: [ arriba ]
@@ -376,11 +377,13 @@ functionality:
       path: test.sh
     - type: file
       path: test_data
-platforms:
+engines:
   - type: docker
     image: quay.io/biocontainers/arriba:2.4.0--h0033a41_2
     setup:
       - type: docker
         run: |
           arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
-  - type: nextflow
+runners:
+  - type: executable
+  - type: nextflow

src/bgzip/config.vsh.yaml

@@ -1,11 +1,11 @@
 functionality:
   name: bgzip
   description: Block compression/decompression utility
-  info:
+  links:
     homepage: https://www.htslib.org/
     documentation: https://www.htslib.org/doc/bgzip.html
     repository: https://github.com/samtools/htslib
-    licence: MIT
+  license: MIT
   requirements:
     commands: [ bgzip ]
   argument_groups:
@@ -115,11 +115,13 @@ functionality:
     - type: file
       path: test_data
 
-platforms:
+engines:
   - type: docker
     image: quay.io/biocontainers/htslib:1.19--h81da01d_0
     setup:
       - type: docker
         run: |
           bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
   - type: nextflow

src/busco/config.vsh.yaml

@@ -1,13 +1,14 @@
 functionality:
   name: busco
   description: Assessment of genome assembly and annotation completeness with single copy orthologs
-  info:
-    keywords: [Genome assembly, quality control]
+  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: "10.1007/978-1-4939-9173-0_14"
-    licence: MIT
+  reference:
+    doi: "10.1007/978-1-4939-9173-0_14"
+  license: MIT
   argument_groups:
     - name: Inputs
       arguments:
@@ -199,11 +200,13 @@ functionality:
       path: test.sh
     - type: file
       path: test_data
-platforms:
+engines:
   - type: docker
     image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |
           busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
   - type: nextflow

src/fastp/config.vsh.yaml

@@ -20,12 +20,13 @@ functionality:
       - support reading from STDIN and writing to STDOUT
       - support interleaved input
       - support ultra-fast FASTQ-level deduplication
-  info:
-    keywords: [RNA-Seq, Trimming, Quality control]
+  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
+  reference:
+    doi: "10.1093/bioinformatics/bty560"
+  licence: MIT
   argument_groups:
     - name: Inputs
       description: |
@@ -564,11 +565,13 @@ functionality:
       path: test.sh
     - type: file
       path: test_data
-platforms:
+engines:
   - type: docker
     image: quay.io/biocontainers/fastp:0.23.4--hadf994f_2
     setup:
       - type: docker
         run: |
           fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
+runners:
+  - type: executable
   - type: nextflow

src/featurecounts/config.vsh.yaml

@@ -2,13 +2,14 @@ functionality:
   name: featurecounts
   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.
-  info:
-    keywords: ["Read counting", "Genomic features"]
+  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 
+  reference:
+    doi: "10.1093/bioinformatics/btt656"
+  licence: GPL-3.0 
   requirements:
     commands: [ featureCounts ]
 
@@ -327,11 +328,13 @@ functionality:
     - type: file
       path: test_data
 
-platforms: 
+engines: 
   - type: docker
     image: quay.io/biocontainers/subread:2.0.6--he4a0461_0
     setup:
       - type: docker
         run: |
           featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
+runners:
+  - type: executable
   - type: nextflow