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[automated] Update json files and markdown cache
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nf-core-bot committed Jan 16, 2025
1 parent f244f29 commit c97a4ac
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242 changes: 242 additions & 0 deletions public/components.json
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}
]
},
{
"name": "agat_convertbed2gff",
"path": "modules/nf-core/agat/convertbed2gff/meta.yml",
"type": "module",
"meta": {
"name": "agat_convertbed2gff",
"description": "Takes a bed12 file and converts to a GFF3 file\n",
"keywords": [
"genome",
"bed",
"gff",
"conversion"
],
"tools": [
{
"agat": {
"description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files",
"homepage": "https://github.com/NBISweden/AGAT",
"documentation": "https://agat.readthedocs.io/",
"tool_dev_url": "https://github.com/NBISweden/AGAT",
"doi": "10.5281/zenodo.3552717",
"licence": [
"GPL v3"
],
"identifier": "biotools:AGAT"
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
}
},
{
"bed": {
"type": "file",
"description": "Input bed12 file",
"pattern": "*.bed"
}
}
]
],
"output": [
{
"gff": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information"
}
},
{
"*.gff": {
"type": "file",
"description": "Output GFF3 file",
"pattern": "*.{gff}"
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@GallVp"
],
"maintainers": [
"@GallVp"
]
}
},
{
"name": "agat_convertspgff2gtf",
"path": "modules/nf-core/agat/convertspgff2gtf/meta.yml",
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"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
Expand Down Expand Up @@ -27896,6 +27983,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
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}
]
},
{
"name": "immunedeconv",
"path": "modules/nf-core/immunedeconv/meta.yml",
"type": "module",
"meta": {
"name": "immunedeconv",
"description": "Perform immune cell deconvolution using RNA-seq data and various computational methods.",
"keywords": [
"Immune Deconvolution",
"RNA-seq",
"Bioinformatics Tools",
"Computational Immunology"
],
"tools": [
{
"immunedeconv": {
"description": "The immunedeconv R package provides functions for immune cell deconvolution\nfrom RNA-seq data. It supports multiple deconvolution methods and generates\nresults as well as visualizations.\n",
"homepage": "https://github.com/icbi-lab/immunedeconv",
"documentation": "https://icbi-lab.github.io/immunedeconv/",
"licence": [
"GPL-2"
]
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"input_file": {
"type": "file",
"description": "Input matrix with genes in rows and samples in columns.",
"pattern": "*.tsv"
}
},
{
"method": {
"type": "string",
"description": "The deconvolution method to use (e.g., 'CIBERSORT', 'EPIC', 'xCell')."
}
},
{
"function": {
"type": "string",
"description": "The specific function from immunedeconv to execute for analysis."
}
}
],
[
{
"gene_symbol_col": {
"type": "string",
"description": "Column name for gene symbols in the matrix input file."
}
}
]
],
"output": [
{
"deconv_table": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.deconvolution_results.tsv": {
"type": "file",
"description": "Results table containing deconvolution data.",
"pattern": "*.deconvolution_results.tsv"
}
}
]
},
{
"deconv_plots": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.png": {
"type": "file",
"description": "Visualization plots generated during deconvolution.",
"pattern": "*.png"
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@grst",
"@nschcolnicov"
],
"maintainers": [
"@grst",
"@nschcolnicov"
]
}
},
{
"name": "instrain_compare",
"path": "modules/nf-core/instrain/compare/meta.yml",
Expand Down Expand Up @@ -108651,6 +108861,22 @@
"name": "pathogensurveillance",
"version": "dev"
},
{
"name": "phyloplace",
"version": "1.0.0"
},
{
"name": "ampliseq",
"version": "2.12.0"
},
{
"name": "multiplesequencealign",
"version": "1.0.0"
},
{
"name": "pathogensurveillance",
"version": "dev"
},
{
"name": "phyloplace",
"version": "1.0.0"
Expand Down Expand Up @@ -115023,6 +115249,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
Expand Down Expand Up @@ -134111,6 +134341,10 @@
"name": "viralrecon",
"version": "2.6.0"
},
{
"name": "viralrecon",
"version": "2.6.0"
},
{
"name": "viralrecon",
"version": "2.6.0"
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"name": "phageannotator",
"version": "dev"
},
{
"name": "phageannotator",
"version": "dev"
},
{
"name": "phageannotator",
"version": "dev"
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"name": "riboseq",
"version": "1.0.1"
},
{
"name": "riboseq",
"version": "1.0.1"
},
{
"name": "riboseq",
"version": "1.0.1"
Expand Down
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