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 Oct 23, 2024
1 parent 09cfed2 commit 85757cf
Show file tree
Hide file tree
Showing 4 changed files with 414 additions and 30 deletions.
Binary file modified .cache.tar.xz
View file
Binary file not shown.
206 changes: 206 additions & 0 deletions public/components.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7792,6 +7792,10 @@
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
Expand Down Expand Up @@ -25650,6 +25654,14 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
Expand Down Expand Up @@ -107768,6 +107780,10 @@
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
Expand Down Expand Up @@ -126296,6 +126312,177 @@
]
}
},
{
"name": "parabricks_fq2bammeth",
"path": "modules/nf-core/parabricks/fq2bammeth/meta.yml",
"type": "module",
"meta": {
"name": "parabricks_fq2bammeth",
"description": "VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence",
"keywords": [
"align",
"sort",
"bqsr",
"duplicates",
"bwameth"
],
"tools": [
{
"parabricks": {
"description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools",
"homepage": "https://www.nvidia.com/en-us/clara/genomics/",
"documentation": "https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html#fq2bam-meth-reference",
"licence": [
"custom"
],
"identifier": ""
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
}
},
{
"reads": {
"type": "file",
"description": "fastq.gz files",
"pattern": "*.fastq.gz"
}
}
],
[
{
"meta2": {
"type": "map",
"description": "Groovy Map containing fasta information\n"
}
},
{
"fasta": {
"type": "file",
"description": "reference fasta file - must be unzipped",
"pattern": "*.fasta"
}
}
],
[
{
"meta3": {
"type": "map",
"description": "Groovy Map containing index information\n"
}
},
{
"index": {
"type": "file",
"description": "reference BWA index",
"pattern": "*.{amb,ann,bwt,pac,sa}"
}
}
],
[
{
"known_sites": {
"type": "file",
"description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.",
"pattern": "*.vcf.gz"
}
}
]
],
"output": [
{
"bam": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
}
},
{
"*.bam": {
"type": "file",
"description": "Sorted BAM file",
"pattern": "*.bam"
}
}
]
},
{
"bai": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
}
},
{
"*.bai": {
"type": "file",
"description": "index corresponding to sorted BAM file",
"pattern": "*.bai"
}
}
]
},
{
"qc_metrics": [
{
"qc_metrics": {
"type": "directory",
"description": "(optional) optional directory of qc metrics",
"pattern": "qc_metrics"
}
}
]
},
{
"bqsr_table": [
{
"*.table": {
"type": "file",
"description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr",
"pattern": "*.table"
}
}
]
},
{
"duplicate_metrics": [
{
"duplicate-metrics.txt": {
"type": "file",
"description": "(optional) metrics calculated from marking duplcates in the bam file",
"pattern": "*-duplicate-metrics.txt"
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@sateeshperi"
],
"maintainers": [
"@sateeshperi"
]
}
},
{
"name": "parabricks_genotypegvcf",
"path": "modules/nf-core/parabricks/genotypegvcf/meta.yml",
Expand Down Expand Up @@ -142524,6 +142711,13 @@
"pattern": "*.{bai}"
}
},
{
"bamlist": {
"type": "file",
"description": "(Optional) File with list of BAM/CRAM files to impute. One file per line.",
"pattern": "*.{txt}"
}
},
{
"reference_haplotype_file": {
"type": "file",
Expand Down Expand Up @@ -199035,6 +199229,10 @@
"name": "datasync",
"version": "dev"
},
{
"name": "deepmodeloptim",
"version": "dev"
},
{
"name": "demo",
"version": "1.0.1"
Expand Down Expand Up @@ -199296,6 +199494,10 @@
"name": "datasync",
"version": "dev"
},
{
"name": "deepmodeloptim",
"version": "dev"
},
{
"name": "demo",
"version": "1.0.1"
Expand Down Expand Up @@ -199545,6 +199747,10 @@
"name": "createtaxdb",
"version": "dev"
},
{
"name": "deepmodeloptim",
"version": "dev"
},
{
"name": "demo",
"version": "1.0.1"
Expand Down
2 changes: 1 addition & 1 deletion public/pipeline_names.json
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]}
{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","deepmodeloptim","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]}
Loading

0 comments on commit 85757cf

Please sign in to comment.