CI
93f55cc2ee
Build pipeline: viash-hub.biobox.main-dkgvl
Source commit: ad89f43726
Source message: Add authors to package config and update author information (#180)
* Add authors to package config and update author information
* update changelog
* add linkedin
374 lines
15 KiB
JSON
374 lines
15 KiB
JSON
{
|
|
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
|
"title": "sortmerna",
|
|
"description": "Local sequence alignment tool for filtering, mapping and clustering. The main \napplication of SortMeRNA is filtering rRNA from metatranscriptomic data.\n",
|
|
"type": "object",
|
|
"$defs": {
|
|
"input": {
|
|
"title": "Input",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"paired": {
|
|
"type": "boolean",
|
|
"description": "Reads are paired-end",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"input": {
|
|
"type": "array",
|
|
"items": {
|
|
"type": "string"
|
|
},
|
|
"format": "path",
|
|
"description": "Input fastq",
|
|
"help_text": "Type: `file`, multiple: `True`, direction: `input`. "
|
|
},
|
|
"ref": {
|
|
"type": "array",
|
|
"items": {
|
|
"type": "string"
|
|
},
|
|
"format": "path",
|
|
"description": "Reference fasta file(s) for rRNA database.",
|
|
"help_text": "Type: `file`, multiple: `True`, direction: `input`. "
|
|
},
|
|
"ribo_database_manifest": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.",
|
|
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
|
|
}
|
|
}
|
|
},
|
|
"output": {
|
|
"title": "Output",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"log": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Sortmerna log file.",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log.log\"`, direction: `output`, example: `\"$id.sortmerna.log\"`. ",
|
|
"default": "$id.$key.log.log"
|
|
},
|
|
"output": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Directory and file prefix for aligned output",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ",
|
|
"default": "$id.$key.output"
|
|
},
|
|
"other": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Create Non-aligned reads output file with this path/prefix",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.other\"`, direction: `output`. ",
|
|
"default": "$id.$key.other"
|
|
}
|
|
}
|
|
},
|
|
"options": {
|
|
"title": "Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"kvdb": {
|
|
"type": "string",
|
|
"description": "Path to directory of the key-value database file, used for storing the alignment results.",
|
|
"help_text": "Type: `string`, multiple: `False`. "
|
|
},
|
|
"idx_dir": {
|
|
"type": "string",
|
|
"description": "Path to the directory for storing the reference index files.",
|
|
"help_text": "Type: `string`, multiple: `False`. "
|
|
},
|
|
"readb": {
|
|
"type": "string",
|
|
"description": "Path to the directory for storing pre-processed reads.",
|
|
"help_text": "Type: `string`, multiple: `False`. "
|
|
},
|
|
"fastx": {
|
|
"type": "boolean",
|
|
"description": "Output aligned reads into FASTA/FASTQ file",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sam": {
|
|
"type": "boolean",
|
|
"description": "Output SAM alignment for aligned reads.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sq": {
|
|
"type": "boolean",
|
|
"description": "Add SQ tags to the SAM file",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"blast": {
|
|
"type": "string",
|
|
"description": "Blast options:\n* '0' - pairwise\n* '1' - tabular(Blast - m 8 format)\n* '1 cigar' - tabular + column for CIGAR\n* '1 cigar qcov' - tabular + columns for CIGAR and query coverage\n* '1 cigar qcov qstrand' - tabular + columns for CIGAR, query coverage and strand\n",
|
|
"help_text": "Type: `string`, multiple: `False`, choices: ``0`, `1`, `1 cigar`, `1 cigar qcov`, `1 cigar qcov qstrand``. ",
|
|
"enum": [
|
|
"0",
|
|
"1",
|
|
"1 cigar",
|
|
"1 cigar qcov",
|
|
"1 cigar qcov qstrand"
|
|
]
|
|
},
|
|
"num_alignments": {
|
|
"type": "integer",
|
|
"description": "Report first INT alignments per read reaching E-value",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `0`. "
|
|
},
|
|
"min_lis": {
|
|
"type": "integer",
|
|
"description": "search all alignments having the first INT longest LIS",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
|
|
},
|
|
"print_all_reads": {
|
|
"type": "boolean",
|
|
"description": "output null alignment strings for non-aligned reads to SAM and/or BLAST tabular files.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"paired_in": {
|
|
"type": "boolean",
|
|
"description": "In the case where a pair of reads is aligned with a score above the threshold, the output of the reads is controlled\nby the following options:\n* --paired_in and --paired_out are both false: Only one read per pair is output to the aligned fasta file.\n* --paired_in is true and --paired_out is false: Both reads of the pair are output to the aligned fasta file.\n* --paired_in is false and --paired_out is true: Both reads are output the the other fasta file (if it is specified).\n",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"paired_out": {
|
|
"type": "boolean",
|
|
"description": "See description of --paired_in.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"out2": {
|
|
"type": "boolean",
|
|
"description": "Output paired reads into separate files",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sout": {
|
|
"type": "boolean",
|
|
"description": "Separate paired and singleton aligned reads",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"zip_out": {
|
|
"type": "string",
|
|
"description": "Compress the output files",
|
|
"help_text": "Type: `string`, multiple: `False`, example: `\"-1\"`, choices: ``1`, `true`, `t`, `yes`, `y`, `0`, `false`, `f`, `no`, `n`, `-1``. ",
|
|
"enum": [
|
|
"1",
|
|
"true",
|
|
"t",
|
|
"yes",
|
|
"y",
|
|
"0",
|
|
"false",
|
|
"f",
|
|
"no",
|
|
"n",
|
|
"-1"
|
|
]
|
|
},
|
|
"match": {
|
|
"type": "integer",
|
|
"description": "Smith-Waterman score for a match (positive integer)",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
|
|
},
|
|
"mismatch": {
|
|
"type": "integer",
|
|
"description": "Smith-Waterman penalty for a mismatch (negative integer)",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `-3`. "
|
|
},
|
|
"gap_open": {
|
|
"type": "integer",
|
|
"description": "Smith-Waterman penalty for introducing a gap (positive integer)",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `5`. "
|
|
},
|
|
"gap_ext": {
|
|
"type": "integer",
|
|
"description": "Smith-Waterman penalty for extending a gap (positive integer)",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
|
|
},
|
|
"N": {
|
|
"type": "integer",
|
|
"description": "Smith-Waterman penalty for ambiguous letters (N's) scored as --mismatch",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `-1`. "
|
|
},
|
|
"a": {
|
|
"type": "integer",
|
|
"description": "Number of threads to use",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
|
|
},
|
|
"e": {
|
|
"type": "number",
|
|
"description": "E-value threshold",
|
|
"help_text": "Type: `double`, multiple: `False`, example: `1.0`. "
|
|
},
|
|
"F": {
|
|
"type": "boolean",
|
|
"description": "Search only the forward strand.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"R": {
|
|
"type": "boolean",
|
|
"description": "Search only the reverse-complementary strand.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"num_alignment": {
|
|
"type": "integer",
|
|
"description": "Report first INT alignments per read reaching E-value (--num_alignments 0 signifies all alignments will be output).\nDefault: '-1'\n",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `-1`. "
|
|
},
|
|
"best": {
|
|
"type": "integer",
|
|
"description": "Report INT best alignments per read reaching E-value by searching --min_lis INT candidate alignments (--best 0\nsignifies all candidate alignments will be searched) Default: '1'.\n",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
|
|
},
|
|
"verbose": {
|
|
"type": "boolean",
|
|
"description": "Verbose output.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"otu picking options": {
|
|
"title": "OTU picking options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"id": {
|
|
"type": "number",
|
|
"description": "%id similarity threshold (the alignment must still pass the E-value threshold)",
|
|
"help_text": "Type: `double`, multiple: `False`, example: `0.97`. "
|
|
},
|
|
"coverage": {
|
|
"type": "number",
|
|
"description": "%query coverage threshold (the alignment must still pass the E-value threshold)",
|
|
"help_text": "Type: `double`, multiple: `False`, example: `0.97`. "
|
|
},
|
|
"de_novo": {
|
|
"type": "boolean",
|
|
"description": "FASTA/FASTQ file for reads matching database < %id off (set using --id) and < %cov (set using --coverage)\n(alignment must still pass the E-value threshold).\n",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"otu_map": {
|
|
"type": "boolean",
|
|
"description": "Output OTU map (input to QIIME's make_otu_table.py).\n",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"advanced options": {
|
|
"title": "Advanced options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"num_seed": {
|
|
"type": "integer",
|
|
"description": "Number of seeds matched before searching for candidate LIS",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
|
|
},
|
|
"passes": {
|
|
"type": "array",
|
|
"items": {
|
|
"type": "integer"
|
|
},
|
|
"description": "Three intervals at which to place the seed on the read L,L/2,3 (L is the seed length set in ./indexdb_rna).\n",
|
|
"help_text": "Type: `integer`, multiple: `True`. "
|
|
},
|
|
"edge": {
|
|
"type": "string",
|
|
"description": "The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the\nreference sequence before performing Smith-Waterman alignment",
|
|
"help_text": "Type: `string`, multiple: `False`, example: `\"4\"`. "
|
|
},
|
|
"full_search": {
|
|
"type": "boolean",
|
|
"description": "Search for all 0-error and 1-error seed off matches in the index rather than stopping after finding a 0-error match\n(<1% gain in sensitivity with up four-fold decrease in speed).\n",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"indexing options": {
|
|
"title": "Indexing Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"index": {
|
|
"type": "integer",
|
|
"description": "Create index files for the reference database",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `2`, choices: ``0`, `1`, `2``. ",
|
|
"enum": [
|
|
0,
|
|
1,
|
|
2
|
|
]
|
|
},
|
|
"-L": {
|
|
"type": "number",
|
|
"description": "Indexing seed length",
|
|
"help_text": "Type: `double`, multiple: `False`, example: `18.0`. "
|
|
},
|
|
"interval": {
|
|
"type": "integer",
|
|
"description": "Index every Nth L-mer in the reference database",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
|
|
},
|
|
"max_pos": {
|
|
"type": "integer",
|
|
"description": "Maximum number of positions to store for each unique L-mer",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `1000`. "
|
|
}
|
|
}
|
|
},
|
|
"nextflow input-output arguments": {
|
|
"title": "Nextflow input-output arguments",
|
|
"type": "object",
|
|
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
|
"properties": {
|
|
"publish_dir": {
|
|
"type": "string",
|
|
"description": "Path to an output directory.",
|
|
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
|
}
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
{
|
|
"$ref": "#/$defs/input"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/output"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/otu picking options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/advanced options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/indexing options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|