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[automated] Update json files and markdown cache
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nf-core-bot committed Oct 26, 2024
1 parent 1ad3e92 commit 5822147
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242 changes: 209 additions & 33 deletions public/components.json
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Expand Up @@ -7822,6 +7822,10 @@
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
Expand Down Expand Up @@ -25728,6 +25732,14 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
Expand Down Expand Up @@ -90998,6 +91010,166 @@
}
]
},
{
"name": "irescue",
"path": "modules/nf-core/irescue/meta.yml",
"type": "module",
"meta": {
"name": "irescue",
"description": "Quantification of transposable elements expression in scRNA-seq",
"keywords": [
"scRNA-seq",
"transposons",
"repeats"
],
"tools": [
{
"irescue": {
"description": "IRescue is a tool for uncertainty-aware quantification of transposable elements expression in scRNA-seq",
"homepage": "https://pypi.org/project/IRescue",
"documentation": "https://pypi.org/project/IRescue",
"tool_dev_url": "https://github.com/bodegalab/irescue",
"doi": "10.1093/nar/gkae793",
"licence": [
"MIT"
],
"identifier": "biotools:irescue"
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"bam": {
"type": "file",
"description": "Sorted BAM file",
"pattern": "*.bam",
"ontologies": [
{
"edam": "http://edamontology.org/format_2572"
}
]
}
}
],
[
{
"genome": {
"type": "string",
"description": "Genome assembly symbol. Not used when bed file is provided.\nIn this case, it can be any value or an empty string.\n"
}
}
],
[
{
"bed": {
"type": "file",
"description": "Bed file of repeats genomic coordinates (optional).",
"pattern": "*.bed",
"ontologies": [
{
"edam": "http://edamontology.org/format_3003"
}
]
}
}
]
],
"output": [
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
},
{
"results": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"${prefix}": {
"type": "directory",
"description": "Folder containing count matrices and logs",
"pattern": "${prefix}"
}
}
]
},
{
"counts": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"${prefix}/counts": {
"type": "directory",
"description": "Folder containing count matrices",
"pattern": "${prefix}/counts"
}
}
]
},
{
"log": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"${prefix}/irescue.log": {
"type": "file",
"description": "Text file contianing run informations",
"pattern": "${prefix}/irescue.log"
}
}
]
},
{
"tmp": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"${prefix}/tmp": {
"type": "directory",
"description": "Folder containing temporary files,\nif kept using the \"--keeptmp\" argument (optional).\n",
"pattern": "${prefix}/tmp"
}
}
]
}
],
"authors": [
"@bepoli"
],
"maintainers": [
"@bepoli"
]
}
},
{
"name": "islandpath",
"path": "modules/nf-core/islandpath/meta.yml",
Expand Down Expand Up @@ -107920,6 +108092,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
Expand Down Expand Up @@ -170246,6 +170422,35 @@
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n"
}
},
{
"collected_crams": {
"type": "file",
"description": "List of sorted BAM/CRAM/SAM file",
"pattern": "*.{bam,cram,sam}"
}
},
{
"collected_crais": {
"type": "file",
"description": "List of BAM/CRAM/SAM index files",
"pattern": "*.{bai,crai,sai}"
}
},
{
"cramlist": {
"type": "file",
"description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n",
"pattern": "*.txt"
}
}
],
[
{
"meta2": {
"type": "map",
"description": "Groovy Map containing information about the set of positions to run the imputation over\ne.g. `[ id:'test' ]`\n"
}
Expand Down Expand Up @@ -170290,35 +170495,6 @@
}
}
],
[
{
"meta2": {
"type": "map",
"description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n"
}
},
{
"collected_crams": {
"type": "file",
"description": "List of sorted BAM/CRAM/SAM file",
"pattern": "*.{bam,cram,sam}"
}
},
{
"collected_crais": {
"type": "file",
"description": "List of BAM/CRAM/SAM index files",
"pattern": "*.{bai,crai,sai}"
}
},
{
"cramlist": {
"type": "file",
"description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n",
"pattern": "*.txt"
}
}
],
[
{
"meta3": {
Expand Down Expand Up @@ -200045,6 +200221,10 @@
"name": "smrnaseq",
"version": "2.4.0"
},
{
"name": "spatialvi",
"version": "dev"
},
{
"name": "variantbenchmarking",
"version": "dev"
Expand Down Expand Up @@ -200280,10 +200460,6 @@
"name": "seqinspector",
"version": "dev"
},
{
"name": "spatialvi",
"version": "dev"
},
{
"name": "taxprofiler",
"version": "1.2.0"
Expand Down
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