Skip to content

Commit

Permalink
[automated] Update json files and markdown cache
Browse files Browse the repository at this point in the history
  • Loading branch information
@nf-core-bot
nf-core-bot committed Jan 13, 2025
1 parent 97fcb1e commit 1354c93
Show file tree
Hide file tree
Showing 3 changed files with 356 additions and 120 deletions.
Binary file modified .cache.tar.xz
View file
Binary file not shown.
201 changes: 201 additions & 0 deletions public/components.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8597,6 +8597,10 @@
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
Expand Down Expand Up @@ -27856,6 +27860,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
Expand Down Expand Up @@ -108443,6 +108451,22 @@
"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 @@ -114795,6 +114819,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
Expand Down Expand Up @@ -133863,6 +133891,10 @@
"name": "viralrecon",
"version": "2.6.0"
},
{
"name": "viralrecon",
"version": "2.6.0"
},
{
"name": "viralrecon",
"version": "2.6.0"
Expand Down Expand Up @@ -150457,6 +150489,167 @@
]
}
},
{
"name": "pypgx_runngspipeline",
"path": "modules/nf-core/pypgx/runngspipeline/meta.yml",
"type": "module",
"meta": {
"name": "pypgx_runngspipeline",
"description": "PyPGx pharmacogenomics genotyping pipeline for NGS data.",
"keywords": [
"pypgx",
"pharmacogenetics",
"genotyping"
],
"tools": [
{
"pypgx": {
"description": "A Python package for pharmacogenomics research",
"homepage": "https://pypgx.readthedocs.io/en/latest/",
"documentation": "https://pypgx.readthedocs.io/en/latest/",
"tool_dev_url": "https://github.com/sbslee/pypgx",
"doi": "10.1371/journal.pone.0272129",
"licence": [
"MIT"
],
"identifier": ""
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n"
}
},
{
"vcf": {
"type": "file",
"description": "BGZIP compressed VCF file with SNVs/indels. Output of pypgx/createinputvcf.",
"pattern": "*.{vcf.gz}"
}
},
{
"tbi": {
"type": "file",
"description": "VCF tabix index.",
"pattern": "*.{vcf.gz.tbi}"
}
},
{
"coverage": {
"type": "file",
"description": "ZIP compressed file with depth of coverage information. Output of pypgx/preparedepthofcoverage. Coverage information is only required when running the module on a pharmacogene with known structural variants.",
"pattern": "*.{zip}"
}
},
{
"control_stats": {
"type": "file",
"description": "ZIP compressed file with control statistics. Output of pypgx/computecontrolstatistics. Control statistics are only required when running the module on a pharmacogene with known structural variants."
}
},
{
"pgx_gene": {
"type": "string",
"description": "Pharmacogene to genotype/phenotype. A list of supported genes is available in the pypgx documentation \"https://pypgx.readthedocs.io/en/latest/genes.html\""
}
}
],
[
{
"meta2": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n"
}
},
{
"resource_bundle": {
"type": "directory",
"description": "Path to the pypgx resource bundle (https://github.com/sbslee/pypgx-bundle)."
}
}
],
[
{
"assembly_version": {
"type": "string",
"description": "Genome assembly version to use."
}
}
]
],
"output": [
{
"results": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*pypgx_output/results.zip": {
"type": "file",
"description": "Main output file of the pipeline in ZIP format, containing a table with star-alleles per sample and CNV calls where applicable."
}
}
]
},
{
"cnv_calls": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*pypgx_output/cnv-calls.zip": {
"type": "file",
"description": "Optional output file in ZIP format, containing CNV calls per sample."
}
}
]
},
{
"consolidated_variants": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*pypgx_output/consolidated-variants.zip": {
"type": "file",
"description": "Output file in ZIP format, containing a consolidated (and phased) VCF file."
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@jorivansteenbrugge"
],
"maintainers": [
"@jorivansteenbrugge"
]
}
},
{
"name": "pyrodigal",
"path": "modules/nf-core/pyrodigal/meta.yml",
Expand Down Expand Up @@ -208756,6 +208949,10 @@
"name": "phageannotator",
"version": "dev"
},
{
"name": "phageannotator",
"version": "dev"
},
{
"name": "phageannotator",
"version": "dev"
Expand Down Expand Up @@ -212482,6 +212679,10 @@
"name": "riboseq",
"version": "1.0.1"
},
{
"name": "riboseq",
"version": "1.0.1"
},
{
"name": "riboseq",
"version": "1.0.1"
Expand Down
Loading

0 comments on commit 1354c93

Please sign in to comment.