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[automated] Update json files and markdown cache
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@nf-core-bot
nf-core-bot committed Jul 16, 2024
1 parent 53cd39a commit 0b79a3d
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217 changes: 208 additions & 9 deletions public/components.json
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"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
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"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
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"name": "methylseq",
"version": "2.6.0"
},
{
"name": "multiplesequencealign",
"version": "dev"
},
{
"name": "nanoseq",
"version": "3.1.0"
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"name": "isoseq",
"version": "1.1.5"
},
{
"name": "isoseq",
"version": "1.1.5"
},
{
"name": "isoseq",
"version": "1.1.5"
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}
},
{
"sam": {
"alignments": {
"type": "file",
"description": "Alignment files in Tab, Text or MEGAN-compatible SAM format",
"pattern": "*.{tab,txt,sam}"
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"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
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"name": "molkart",
"version": "1.0.0"
},
{
"name": "multiplesequencealign",
"version": "dev"
},
{
"name": "nanoseq",
"version": "3.1.0"
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]
}
},
{
"name": "fastq_qc_trim_filter_setstrandedness",
"path": "subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml",
"type": "subworkflow",
"meta": {
"name": "fastq_qc_trim_filter_setstrandedness",
"description": "Basic FASTQ preprocessing for RNA-seq",
"keywords": [
"fastq",
"rnaseq",
"rrna",
"trimming",
"subsample",
"strandedness"
],
"components": [
"bbmap/bbsplit",
"samtools/sort",
"samtools/index",
"cat",
"cat/fastq",
"sortmerna",
"fastq_subsample_fq_salmon",
"fastq_fastqc_umitools_trimgalore",
"fastq_fastqc_umitools_fastp"
],
"input": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n"
}
},
{
"ch_reads": {
"type": "file",
"description": "Channel with input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively.\n"
}
},
{
"ch_fasta": {
"type": "file",
"description": "Channel with genome sequence in fasta format"
}
},
{
"ch_transcript_fasta": {
"type": "file",
"description": "Channel with transcriptome sequence in fasta format"
}
},
{
"ch_gtf": {
"type": "file",
"description": "Channel with features in GTF format"
}
},
{
"ch_salmon_index": {
"type": "file",
"description": "Directory containing Salmon index"
}
},
{
"ch_sortmerna_index": {
"type": "file",
"description": "Directory containing sortmerna index"
}
},
{
"ch_bbsplit_index": {
"type": "file",
"description": "Path to directory or tar.gz archive for pre-built BBSplit index"
}
},
{
"ch_ribo_db": {
"type": "file",
"description": "Channel with text file containing paths to fasta files (one per line)\nthat will be used to create the database for SortMeRNA\n"
}
},
{
"skip_bbsplit": {
"type": "boolean",
"description": "Whether to skip BBSplit for removal of non-reference genome reads"
}
},
{
"skip_fastqc": {
"type": "boolean",
"description": "Whether to skip FastQC"
}
},
{
"skip_trimming": {
"type": "boolean",
"description": "Whether to skip trimming"
}
},
{
"skip_umi_extract": {
"type": "boolean",
"description": "Skip the UMI extraction from the read in case the UMIs have been moved\nto the headers in advance of the pipeline run\n"
}
},
{
"make_salmon_index": {
"type": "boolean",
"description": "Whether to create salmon index before running salmon quant"
}
},
{
"make_sortmerna_index": {
"type": "boolean",
"description": "Whether to create sortmerna index before running sortmerna"
}
},
{
"trimmer": {
"type": "string",
"description": "Specifies the trimming tool to use - available options are 'trimgalore'\nand 'fastp'\n"
}
},
{
"min_trimmed_reads": {
"type": "integer",
"description": "Minimum number of trimmed reads below which samples are removed from\nfurther processing\n"
}
},
{
"save_trimmed": {
"type": "boolean",
"description": "Save the trimmed FastQ files in the results directory?"
}
},
{
"remove_ribo_rna": {
"type": "boolean",
"description": "Enable the removal of reads derived from ribosomal RNA using SortMeRNA?"
}
},
{
"with_umi": {
"type": "boolean",
"description": "Enable UMI-based read deduplication"
}
},
{
"umi_discard_read": {
"type": "integer",
"description": "After UMI barcode extraction discard either R1 or R2 by setting this\nparameter to 1 or 2, respectively\n"
}
}
],
"output": [
{
"reads": {
"type": "file",
"description": "Preprocessed fastq reads",
"pattern": "*.{fq,fastq}{,.gz}"
}
},
{
"multiqc_files": {
"type": "file",
"description": "MultiQC-compatible output files from tools used in prepreocessing",
"pattern": "*"
}
},
{
"trim_read_count": {
"type": "integer",
"description": "Number of reads remaining after trimming for all input samples"
}
},
{
"versions": {
"type": "file",
"description": "File containing software versions\nStructure: [ path(versions.yml) ]\n",
"pattern": "versions.yml"
}
}
],
"authors": [
"@pinin4fjords"
],
"maintainers": [
"@pinin4fjords"
]
}
},
{
"name": "fastq_subsample_fq_salmon",
"path": "subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml",
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