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 ]