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
489 lines
18 KiB
JSON
489 lines
18 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "cutadapt",
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"description": "Cutadapt removes adapter sequences from high-throughput sequencing reads.\n",
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"type": "object",
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"$defs": {
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"specify adapters for r1": {
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"title": "Specify Adapters for R1",
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"type": "object",
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"description": "No description",
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"properties": {
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"adapter": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter ligated to the 3' end (paired data:\nof the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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},
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"front": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter ligated to the 5' end (paired data:\nof the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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},
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"anywhere": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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}
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}
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},
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"specify adapters using fasta files for r1": {
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"title": "Specify Adapters using Fasta files for R1",
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"type": "object",
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"description": "No description",
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"properties": {
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"adapter_fasta": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"description": "Fasta file containing sequences of an adapter ligated to the 3' end (paired data:\nof the first read)",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`. "
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},
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"front_fasta": {
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"type": "string",
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"format": "path",
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"description": "Fasta file containing sequences of an adapter ligated to the 5' end (paired data:\nof the first read)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"anywhere_fasta": {
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"type": "string",
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"format": "path",
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"description": "Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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}
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}
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},
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"specify adapters for r2": {
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"title": "Specify Adapters for R2",
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"type": "object",
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"description": "No description",
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"properties": {
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"adapter_r2": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter ligated to the 3' end (paired data:\nof the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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},
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"front_r2": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter ligated to the 5' end (paired data:\nof the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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},
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"anywhere_r2": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Sequence of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)",
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"help_text": "Type: `string`, multiple: `True`. "
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}
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}
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},
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"specify adapters using fasta files for r2": {
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"title": "Specify Adapters using Fasta files for R2",
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"type": "object",
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"description": "No description",
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"properties": {
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"adapter_r2_fasta": {
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"type": "string",
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"format": "path",
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"description": "Fasta file containing sequences of an adapter ligated to the 3' end (paired data:\nof the first read)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"front_r2_fasta": {
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"type": "string",
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"format": "path",
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"description": "Fasta file containing sequences of an adapter ligated to the 5' end (paired data:\nof the first read)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"anywhere_r2_fasta": {
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"type": "string",
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"format": "path",
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"description": "Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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}
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}
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},
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"paired-end options": {
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"title": "Paired-end options",
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"type": "object",
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"description": "No description",
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"properties": {
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"pair_adapters": {
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"type": "boolean",
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"description": "Treat adapters given with -a/-A etc",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"pair_filter": {
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"type": "string",
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"description": "Which of the reads in a paired-end read have to match the\nfiltering criterion in order for the pair to be filtered.\n",
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"help_text": "Type: `string`, multiple: `False`, choices: ``any`, `both`, `first``. ",
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"enum": [
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"any",
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"both",
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"first"
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]
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},
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"interleaved": {
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"type": "boolean",
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"description": "Read and/or write interleaved paired-end reads.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"input parameters": {
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"title": "Input parameters",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Input fastq file for single-end reads or R1 for paired-end reads.\n",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"input_r2": {
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"type": "string",
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"format": "path",
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"description": "Input fastq file for R2 in the case of paired-end reads.\n",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"error_rate": {
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"type": "number",
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"description": "Maximum allowed error rate (if 0 <= E < 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger >= 1)",
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"help_text": "Type: `double`, multiple: `False`, example: `0.1`. "
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},
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"no_indels": {
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"type": "boolean",
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"description": "Allow only mismatches in alignments.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"times": {
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"type": "integer",
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"description": "Remove up to COUNT adapters from each read",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"overlap": {
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"type": "integer",
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"description": "Require MINLENGTH overlap between read and adapter for an\nadapter to be found",
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"help_text": "Type: `integer`, multiple: `False`, example: `3`. "
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},
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"match_read_wildcards": {
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"type": "boolean",
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"description": "Interpret IUPAC wildcards in reads.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"no_match_adapter_wildcards": {
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"type": "boolean",
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"description": "Do not interpret IUPAC wildcards in adapters.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"action": {
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"type": "string",
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"description": "What to do if a match was found",
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"help_text": "Type: `string`, multiple: `False`, example: `\"trim\"`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. ",
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"enum": [
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"trim",
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"retain",
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"mask",
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"lowercase",
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"none"
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]
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},
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"revcomp": {
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"type": "boolean",
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"description": "Check both the read and its reverse complement for adapter\nmatches",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"demultiplexing options": {
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"title": "Demultiplexing options",
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"type": "object",
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"description": "No description",
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"properties": {
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"demultiplex_mode": {
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"type": "string",
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"description": "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual', adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs",
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"help_text": "Type: `string`, multiple: `False`, choices: ``single`, `unique_dual`, `combinatorial_dual``. ",
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"enum": [
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"single",
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"unique_dual",
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"combinatorial_dual"
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]
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}
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}
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},
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"read modifications": {
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"title": "Read modifications",
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"type": "object",
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"description": "No description",
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"properties": {
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"cut": {
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"type": "array",
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"items": {
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"type": "integer"
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},
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"description": "Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2)",
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"help_text": "Type: `integer`, multiple: `True`. "
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},
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"cut_r2": {
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"type": "array",
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"items": {
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"type": "integer"
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},
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"description": "Remove LEN bases from each read (for R2)",
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"help_text": "Type: `integer`, multiple: `True`. "
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},
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"nextseq_trim": {
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"type": "string",
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"description": "NextSeq-specific quality trimming (each read)",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"quality_cutoff": {
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"type": "string",
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"description": "Trim low-quality bases from 5' and/or 3' ends of each read\nbefore adapter removal",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"quality_cutoff_r2": {
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"type": "string",
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"description": "Quality-trimming cutoff for R2",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"quality_base": {
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"type": "integer",
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"description": "Assume that quality values in FASTQ are encoded as\nascii(quality + N)",
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"help_text": "Type: `integer`, multiple: `False`, example: `33`. "
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},
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"poly_a": {
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"type": "boolean",
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"description": "Trim poly-A tails",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"length": {
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"type": "integer",
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"description": "Shorten reads to LENGTH",
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"help_text": "Type: `integer`, multiple: `False`. "
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},
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"trim_n": {
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"type": "boolean",
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"description": "Trim N's on ends of reads.",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"length_tag": {
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"type": "string",
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"description": "Search for TAG followed by a decimal number in the\ndescription field of the read",
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"help_text": "Type: `string`, multiple: `False`, example: `\"length=\"`. "
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},
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"strip_suffix": {
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"type": "string",
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"description": "Remove this suffix from read names if present",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"prefix": {
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"type": "string",
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"description": "Add this prefix to read names",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"suffix": {
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"type": "string",
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"description": "Add this suffix to read names; can also include {name}\n",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"rename": {
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"type": "string",
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"description": "Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"zero_cap": {
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"type": "boolean",
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"description": "Change negative quality values to zero.",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"filtering of processed reads": {
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"title": "Filtering of processed reads",
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"type": "object",
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"description": "Filters are applied after above read modifications. Paired-end reads are\nalways discarded pairwise (see also --pair_filter).\n",
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"properties": {
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"minimum_length": {
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"type": "string",
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"description": "Discard reads shorter than LEN",
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"help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. "
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},
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"maximum_length": {
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"type": "string",
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"description": "Discard reads longer than LEN",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"max_n": {
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"type": "string",
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"description": "Discard reads with more than COUNT 'N' bases",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"max_expected_errors": {
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"type": "string",
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"description": "Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS.\n",
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"help_text": "Type: `long`, multiple: `False`. "
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},
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"max_average_error_rate": {
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"type": "string",
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"description": "as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length.\n",
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"help_text": "Type: `long`, multiple: `False`. "
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},
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"discard_trimmed": {
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"type": "boolean",
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"description": "Discard reads that contain an adapter",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"discard_untrimmed": {
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"type": "boolean",
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"description": "Discard reads that do not contain an adapter.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"discard_casava": {
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"type": "boolean",
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"description": "Discard reads that did not pass CASAVA filtering (header\nhas :Y:).\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"output parameters": {
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"title": "Output parameters",
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"type": "object",
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"description": "No description",
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"properties": {
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"report": {
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"type": "string",
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"description": "Which type of report to print: 'full' (default) or 'minimal'.\n",
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"help_text": "Type: `string`, multiple: `False`, example: `\"full\"`, choices: ``full`, `minimal``. ",
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"enum": [
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"full",
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"minimal"
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]
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},
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"json": {
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"type": "boolean",
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"description": "Write report in JSON format to this file.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"output": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"description": "Glob pattern for matching the expected output files.\nShould include `$output_dir`.\n",
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"help_text": "Type: `file`, multiple: `True`, required, default: `\"$id.$key.output_*.fast[a,q]\"`, direction: `output`, example: `[\"fastq/*_001.fast[a,q]\"]`. ",
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"default": "$id.$key.output_*.fast[a,q]"
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},
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"fasta": {
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"type": "boolean",
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"description": "Output FASTA to standard output even on FASTQ input.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"info_file": {
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"type": "boolean",
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"description": "Write information about each read and its adapter matches\ninto info.txt in the output directory.\nSee the documentation for the file format.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"debug": {
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"title": "Debug",
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"type": "object",
|
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"description": "No description",
|
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"properties": {
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"debug": {
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"type": "boolean",
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"description": "Print debug information",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"nextflow input-output arguments": {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"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.",
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"properties": {
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"publish_dir": {
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"type": "string",
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"description": "Path to an output directory.",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/$defs/specify adapters for r1"
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},
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{
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"$ref": "#/$defs/specify adapters using fasta files for r1"
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},
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{
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"$ref": "#/$defs/specify adapters for r2"
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},
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{
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"$ref": "#/$defs/specify adapters using fasta files for r2"
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},
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{
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"$ref": "#/$defs/paired-end options"
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},
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{
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"$ref": "#/$defs/input parameters"
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},
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{
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"$ref": "#/$defs/demultiplexing options"
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},
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{
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"$ref": "#/$defs/read modifications"
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},
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{
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"$ref": "#/$defs/filtering of processed reads"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/output parameters"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/debug"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|