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[automated] Update json files and markdown cache
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nf-core-bot committed Feb 9, 2024
1 parent 063eec4 commit bf54045
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219 changes: 203 additions & 16 deletions public/components.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3994,6 +3994,10 @@
"name": "rnafusion",
"version": "3.0.1"
},
{
"name": "rnafusion",
"version": "3.0.1"
},
{
"name": "rnafusion",
"version": "3.0.1"
Expand Down Expand Up @@ -37377,6 +37381,10 @@
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
Expand Down Expand Up @@ -38798,6 +38806,10 @@
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
Expand Down Expand Up @@ -43371,6 +43383,10 @@
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
},
{
"name": "rnadnavar",
"version": "dev"
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"homepage": "https://github.com/pha4ge/hAMRonization/",
"documentation": "https://github.com/pha4ge/hAMRonization/",
"tool_dev_url": "https://github.com/pha4ge/hAMRonization",
"licence": "['GNU Lesser General Public v3 (LGPL v3)']"
"licence": [
"GNU Lesser General Public v3 (LGPL v3)"
]
}
}
],
Expand All @@ -53256,21 +53274,21 @@
},
{
"format": {
"type": "value",
"type": "string",
"description": "Type of report file to be produced",
"pattern": "tsv|json"
}
},
{
"software_version": {
"type": "value",
"type": "string",
"description": "Version of AMRfinder used",
"pattern": "[0-9].[0-9].[0-9]"
}
},
{
"reference_db_version": {
"type": "value",
"type": "string",
"description": "Database version of ncbi_AMRfinder used",
"pattern": "[0-9]-[0-9]-[0-9].[0-9]"
}
Expand Down Expand Up @@ -53361,21 +53379,21 @@
},
{
"format": {
"type": "value",
"type": "string",
"description": "Type of report file to be produced",
"pattern": "tsv|json"
}
},
{
"software_version": {
"type": "value",
"type": "string",
"description": "Version of DeepARG used",
"pattern": "[0-9].[0-9].[0-9]"
}
},
{
"reference_db_version": {
"type": "value",
"type": "integer",
"description": "Database version of DeepARG used",
"pattern": "[0-9]"
}
Expand Down Expand Up @@ -53446,7 +53464,9 @@
"homepage": "https://github.com/pha4ge/hAMRonization/",
"documentation": "https://github.com/pha4ge/hAMRonization/",
"tool_dev_url": "https://github.com/pha4ge/hAMRonization",
"licence": "['GNU Lesser General Public v3 (LGPL v3)']"
"licence": [
"GNU Lesser General Public v3 (LGPL v3)"
]
}
}
],
Expand All @@ -53466,21 +53486,21 @@
},
{
"format": {
"type": "value",
"type": "string",
"description": "Type of report file to be produced",
"pattern": "tsv|json"
}
},
{
"software_version": {
"type": "value",
"type": "string",
"description": "Version of fARGene used",
"pattern": "[0-9].[0-9].[0-9]"
}
},
{
"reference_db_version": {
"type": "value",
"type": "string",
"description": "Database version of fARGene used",
"pattern": "[0-9].[0-9].[0-9]"
}
Expand Down Expand Up @@ -53551,7 +53571,9 @@
"homepage": "https://github.com/pha4ge/hAMRonization/",
"documentation": "https://github.com/pha4ge/hAMRonization/",
"tool_dev_url": "https://github.com/pha4ge/hAMRonization",
"licence": "['GNU Lesser General Public v3 (LGPL v3)']"
"licence": [
"GNU Lesser General Public v3 (LGPL v3)"
]
}
}
],
Expand All @@ -53571,21 +53593,21 @@
},
{
"format": {
"type": "value",
"type": "string",
"description": "Type of report file to be produced",
"pattern": "tsv|json"
}
},
{
"software_version": {
"type": "value",
"type": "string",
"description": "Version of DeepARG used",
"pattern": "[0-9].[0-9].[0-9]"
}
},
{
"reference_db_version": {
"type": "value",
"type": "string",
"description": "Database version of DeepARG used",
"pattern": "[0-9].[0-9].[0-9]"
}
Expand Down Expand Up @@ -53669,7 +53691,7 @@
},
{
"format": {
"type": "value",
"type": "string",
"description": "Type of final combined report file to be produced",
"pattern": "tsv|json|interactive"
}
Expand Down Expand Up @@ -109950,6 +109972,159 @@
]
}
},
{
"name": "tximeta_tximport",
"path": "modules/nf-core/tximeta/tximport/meta.yml",
"type": "module",
"meta": {
"name": "tximeta_tximport",
"description": "Import transcript-level abundances and estimated counts for gene-level\nanalysis packages\n",
"keywords": [
"gene",
"kallisto",
"pseudoalignment",
"salmon",
"transcript"
],
"tools": [
{
"tximeta": {
"description": "Transcript Quantification Import with Automatic Metadata",
"homepage": "https://bioconductor.org/packages/release/bioc/html/tximeta.html",
"documentation": "https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html",
"tool_dev_url": "https://github.com/thelovelab/tximeta",
"doi": "10.1371/journal.pcbi.1007664",
"licence": [
"GPL-2"
]
}
}
],
"input": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n"
}
},
{
"quants": {
"type": "directory",
"description": "Paths to subdirectories corresponding to sample-wise runs of Salmon or Kallisto"
}
},
{
"meta2": {
"type": "map",
"description": "Groovy Map containing reference information related to the species\nreference e.g. `[ id:'yeast' ]`\n"
}
},
{
"tx2gene": {
"type": "file",
"description": "A transcript to gene mapping table such as those generated by custom/tx2gene",
"pattern": "*.{csv,tsv}"
}
},
{
"meta3": {
"type": "map",
"description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n"
}
},
{
"coldata": {
"type": "file",
"description": "Optional 'coldata' file equivalent to a sample sheet where the first\ncolumn corresponds to the sample names (directory names in the input\nsalmon/ kallisto results)\n",
"pattern": "*.{csv,tsv}"
}
},
{
"quant_type": {
"type": "string",
"description": "Quantification type, 'kallisto' or 'salmon'"
}
}
],
"output": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n"
}
},
{
"tpm_gene": {
"type": "file",
"description": "Abundance (TPM) values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n",
"pattern": "*gene_tpm.tsv"
}
},
{
"counts_gene": {
"type": "file",
"description": "Count values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n",
"pattern": "*gene_counts.tsv"
}
},
{
"counts_gene_length_scaled": {
"type": "file",
"description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'lengthScaledTPM'\n",
"pattern": "*gene_counts_length_scaled.tsv"
}
},
{
"counts_gene_scaled": {
"type": "file",
"description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'scaledTPM'\n",
"pattern": "*gene_counts_scaled.tsv"
}
},
{
"gene_lengths": {
"type": "file",
"description": "Length values derived from tximport output after summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n",
"pattern": "*gene_lengths.tsv"
}
},
{
"tpm_transcript": {
"type": "file",
"description": "Abundance (TPM) values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n",
"pattern": "*transcript_tpm.tsv"
}
},
{
"counts_transcript": {
"type": "file",
"description": "Count values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n",
"pattern": "*transcript_counts.tsv"
}
},
{
"transcript_lengths": {
"type": "file",
"description": "Length values derived from tximport output without summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n",
"pattern": "*gene_lengths.tsv"
}
},
{
"versions": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
],
"authors": [
"@pinin4fjords"
],
"maintainers": [
"@pinin4fjords"
]
}
},
{
"name": "ucsc_bedclip",
"path": "modules/nf-core/ucsc/bedclip/meta.yml",
Expand Down Expand Up @@ -122183,6 +122358,10 @@
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
Expand Down Expand Up @@ -123020,6 +123199,10 @@
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
Expand Down Expand Up @@ -123890,6 +124073,10 @@
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
},
{
"name": "fetchngs",
"version": "1.11.0"
Expand Down
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