From 5a41cfdcb992d1be5c4ef3500d789e4fe3af4fde Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 12 Feb 2024 07:13:25 +0100 Subject: [PATCH 1/3] uniformize metadata --- src/arriba/config.vsh.yaml | 12 +++++++----- src/bgzip/config.vsh.yaml | 11 ++++++----- src/busco/busco_download_datasets/config.vsh.yaml | 12 +++++++----- src/busco/busco_list_datasets/config.vsh.yaml | 12 +++++++----- src/busco/busco_run/config.vsh.yaml | 12 +++++++----- src/fastp/config.vsh.yaml | 10 ++++++---- src/featurecounts/config.vsh.yaml | 12 +++++++----- src/pear/config.vsh.yaml | 12 +++++++----- 8 files changed, 54 insertions(+), 39 deletions(-) diff --git a/src/arriba/config.vsh.yaml b/src/arriba/config.vsh.yaml index 601ad6c2..922fd21a 100644 --- a/src/arriba/config.vsh.yaml +++ b/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 ] diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml index c37db43c..049d0cbf 100644 --- a/src/bgzip/config.vsh.yaml +++ b/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: diff --git a/src/busco/busco_download_datasets/config.vsh.yaml b/src/busco/busco_download_datasets/config.vsh.yaml index dc356f8a..16cd9b87 100644 --- a/src/busco/busco_download_datasets/config.vsh.yaml +++ b/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: diff --git a/src/busco/busco_list_datasets/config.vsh.yaml b/src/busco/busco_list_datasets/config.vsh.yaml index df612fdc..dc495d37 100644 --- a/src/busco/busco_list_datasets/config.vsh.yaml +++ b/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: diff --git a/src/busco/busco_run/config.vsh.yaml b/src/busco/busco_run/config.vsh.yaml index 0fdfea2e..8524b068 100644 --- a/src/busco/busco_run/config.vsh.yaml +++ b/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: diff --git a/src/fastp/config.vsh.yaml b/src/fastp/config.vsh.yaml index c513ec92..24db55d1 100644 --- a/src/fastp/config.vsh.yaml +++ b/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: | diff --git a/src/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml index 8a2002d4..6779b7e6 100644 --- a/src/featurecounts/config.vsh.yaml +++ b/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 ] diff --git a/src/pear/config.vsh.yaml b/src/pear/config.vsh.yaml index 6bd8fe3c..53921baa 100644 --- a/src/pear/config.vsh.yaml +++ b/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: From 879e6aceeaf226ae0352a70763efcb4aee61d3a0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 12 Feb 2024 07:13:55 +0100 Subject: [PATCH 2/3] remove keywords from helper components --- src/busco/busco_download_datasets/config.vsh.yaml | 1 - src/busco/busco_list_datasets/config.vsh.yaml | 1 - 2 files changed, 2 deletions(-) diff --git a/src/busco/busco_download_datasets/config.vsh.yaml b/src/busco/busco_download_datasets/config.vsh.yaml index 16cd9b87..a592ed89 100644 --- a/src/busco/busco_download_datasets/config.vsh.yaml +++ b/src/busco/busco_download_datasets/config.vsh.yaml @@ -3,7 +3,6 @@ functionality: namespace: busco description: Downloads available busco datasets info: - keywords: [lineage datasets] links: homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html diff --git a/src/busco/busco_list_datasets/config.vsh.yaml b/src/busco/busco_list_datasets/config.vsh.yaml index dc495d37..004628c9 100644 --- a/src/busco/busco_list_datasets/config.vsh.yaml +++ b/src/busco/busco_list_datasets/config.vsh.yaml @@ -3,7 +3,6 @@ functionality: namespace: busco description: Lists the available busco datasets info: - keywords: [lineage datasets] links: homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html From ec8e9e10882c07bcc6e51defddfb59c063db0c8a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 12 Feb 2024 07:14:54 +0100 Subject: [PATCH 3/3] add entry to changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba44f99e..7ca743c6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,8 @@ ## MINOR CHANGES +* Uniformize component metadata (PR #23). + ## DOCUMENTATION ## BUG FIXES \ No newline at end of file