CI
04a5851ff8
Build pipeline: viash-hub.biobox.main-tb4cv
Source commit: 7158daa5f6
Source message: Fix bases2fastq component, update to latest practices (#190)
* wip updates
* refactor component
* assume bases2fastq follows semver
* fix version command
* add entry to changelog
* move to minor changes
688 lines
26 KiB
JSON
688 lines
26 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "bowtie2_align",
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"description": "Align single-end and paired-end reads to a reference genome using Bowtie2.\n\nBowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads\nto long reference sequences. It is particularly good at aligning reads of about\n50 up to 100s of characters, and particularly good at aligning to relatively\nlong (e.g. mammalian) genomes.\n",
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"type": "object",
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"$defs": {
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"inputs": {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"index": {
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"type": "string",
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"description": "Index filename prefix (minus trailing .X.bt2).",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"genome_index\"`. "
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},
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"mate1": {
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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": "Files with #1 mates, paired with files in --mate2.",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads_R1.fastq.gz\"]`. "
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},
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"mate2": {
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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": "Files with #2 mates, paired with files in --mate1.",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads_R2.fastq.gz\"]`. "
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},
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"unpaired": {
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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": "Files with unpaired reads.",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads.fastq.gz\"]`. "
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},
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"interleaved": {
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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": "Files with interleaved paired-end FASTQ/FASTA reads.",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"interleaved.fastq.gz\"]`. "
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},
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"bam_input": {
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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": "Files are unaligned BAM sorted by read name.",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"unaligned.bam\"]`. "
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}
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}
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},
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"outputs": {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type": "string",
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"format": "path",
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"description": "File for SAM output (default stdout).",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.sam\"`, direction: `output`, example: `\"aligned.sam\"`. ",
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"default": "$id.$key.output.sam"
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},
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"un": {
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"type": "string",
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"format": "path",
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"description": "Write unpaired reads that didn't align to file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.un.fastq\"`, direction: `output`, example: `\"unaligned.fastq\"`. ",
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"default": "$id.$key.un.fastq"
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},
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"al": {
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"type": "string",
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"format": "path",
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"description": "Write unpaired reads that aligned at least once to file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.al.fastq\"`, direction: `output`, example: `\"aligned.fastq\"`. ",
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"default": "$id.$key.al.fastq"
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},
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"un_conc": {
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"type": "string",
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"format": "path",
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"description": "Write pairs that didn't align concordantly to file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.un_conc.fastq\"`, direction: `output`, example: `\"unaligned_pairs.fastq\"`. ",
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"default": "$id.$key.un_conc.fastq"
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},
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"al_conc": {
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"type": "string",
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"format": "path",
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"description": "Write pairs that aligned concordantly at least once to file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.al_conc.fastq\"`, direction: `output`, example: `\"aligned_pairs.fastq\"`. ",
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"default": "$id.$key.al_conc.fastq"
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},
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"met_file": {
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"type": "string",
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"format": "path",
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"description": "Send metrics to file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.met_file.txt\"`, direction: `output`, example: `\"metrics.txt\"`. ",
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"default": "$id.$key.met_file.txt"
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}
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}
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},
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"input format options": {
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"title": "Input Format Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"fastq": {
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"type": "boolean",
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"description": "Query input files are FASTQ .fq/.fastq (default).",
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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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"tab5": {
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"type": "boolean",
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"description": "Query input files are TAB5 .tab5.",
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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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"tab6": {
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"type": "boolean",
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"description": "Query input files are TAB6 .tab6.",
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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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"qseq": {
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"type": "boolean",
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"description": "Query input files are in Illumina's qseq format.",
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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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"fasta": {
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"type": "boolean",
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"description": "Query input files are (multi-)FASTA .fa/.mfa.",
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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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"raw": {
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"type": "boolean",
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"description": "Query input files are raw one-sequence-per-line.",
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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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"cmdline": {
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"type": "boolean",
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"description": "<m1>, <m2>, <r> are sequences themselves, not files.",
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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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"skip": {
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"type": "integer",
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"description": "Skip the first <int> reads/pairs in the input.",
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"help_text": "Type: `integer`, multiple: `False`, example: `1000`. "
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},
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"upto": {
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"type": "integer",
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"description": "Stop after first <int> reads/pairs.",
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"help_text": "Type: `integer`, multiple: `False`, example: `10000`. "
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},
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"trim5": {
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"type": "integer",
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"description": "Trim <int> bases from 5'/left end of reads.",
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"help_text": "Type: `integer`, multiple: `False`, example: `5`. "
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},
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"trim3": {
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"type": "integer",
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"description": "Trim <int> bases from 3'/right end of reads.",
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"help_text": "Type: `integer`, multiple: `False`, example: `3`. "
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},
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"trim_to": {
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"type": "string",
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"description": "Trim reads exceeding <int> bases from either 3' or 5' end",
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"help_text": "Type: `string`, multiple: `False`, example: `\"3:100\"`. "
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},
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"continuous_fasta": {
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"type": "string",
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"description": "Query input files are continuous FASTA where reads are k-mers",
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"help_text": "Type: `string`, multiple: `False`, example: `\"k:25,i:1\"`. "
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},
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"phred33": {
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"type": "boolean",
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"description": "Qualities are Phred+33 (default).",
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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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"phred64": {
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"type": "boolean",
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"description": "Qualities are Phred+64.",
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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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"int_quals": {
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"type": "boolean",
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"description": "Qualities encoded as space-delimited integers.",
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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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"alignment presets": {
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"title": "Alignment Presets",
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"type": "object",
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"description": "No description",
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"properties": {
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"very_fast": {
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"type": "boolean",
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"description": "Same as -D 5 -R 1 -N 0 -L 22 -i S,0,2.50.",
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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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"fast": {
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"type": "boolean",
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"description": "Same as -D 10 -R 2 -N 0 -L 22 -i S,0,2.50.",
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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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"sensitive": {
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"type": "boolean",
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"description": "Same as -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default).",
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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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"very_sensitive": {
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"type": "boolean",
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"description": "Same as -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.",
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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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"very_fast_local": {
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"type": "boolean",
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"description": "Same as -D 5 -R 1 -N 0 -L 25 -i S,1,2.00.",
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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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"fast_local": {
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"type": "boolean",
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"description": "Same as -D 10 -R 2 -N 0 -L 22 -i S,1,1.75.",
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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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"sensitive_local": {
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"type": "boolean",
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"description": "Same as -D 15 -R 2 -N 0 -L 20 -i S,1,0.75.",
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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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"very_sensitive_local": {
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"type": "boolean",
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"description": "Same as -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.",
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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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"alignment options": {
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"title": "Alignment Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"N": {
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"type": "integer",
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"description": "Max # mismatches in seed alignment; can be 0 or 1.",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"L": {
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"type": "integer",
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"description": "Length of seed substrings; must be >3, <32.",
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"help_text": "Type: `integer`, multiple: `False`, example: `22`. "
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},
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"i": {
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"type": "string",
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"description": "Interval between seed substrings w/r/t read len.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"S,1,1.15\"`. "
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},
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"n_ceil": {
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"type": "string",
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"description": "Function for max # non-A/C/G/Ts permitted in aln.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"L,0,0.15\"`. "
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},
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"dpad": {
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"type": "integer",
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"description": "Include <int> extra ref chars on sides of DP table.",
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"help_text": "Type: `integer`, multiple: `False`, example: `15`. "
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},
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"gbar": {
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"type": "integer",
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"description": "Disallow gaps within <int> nucs of read extremes.",
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"help_text": "Type: `integer`, multiple: `False`, example: `4`. "
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},
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"ignore_quals": {
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"type": "boolean",
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"description": "Treat all quality values as 30 on Phred scale.",
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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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"nofw": {
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"type": "boolean",
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"description": "Do not align forward (original) version of read.",
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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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"norc": {
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"type": "boolean",
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"description": "Do not align reverse-complement version of read.",
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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_1mm_upfront": {
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"type": "boolean",
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"description": "Do not allow 1 mismatch alignments before attempting to scan for the optimal seeded alignments.",
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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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"end_to_end": {
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"type": "boolean",
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"description": "Entire read must align; no clipping (default).",
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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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"local": {
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"type": "boolean",
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"description": "Local alignment; ends might be soft clipped.",
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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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"scoring options": {
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"title": "Scoring Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"ma": {
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"type": "integer",
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"description": "Match bonus (0 for --end-to-end, 2 for --local).",
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"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
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},
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"mp": {
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"type": "string",
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"description": "Max penalty for mismatch; lower qual = lower penalty.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"6\"`. "
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},
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"np": {
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"type": "integer",
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"description": "Penalty for non-A/C/G/Ts in read/ref.",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"rdg": {
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"type": "string",
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"description": "Read gap open, extend penalties.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"5,3\"`. "
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},
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"rfg": {
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"type": "string",
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"description": "Reference gap open, extend penalties.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"5,3\"`. "
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},
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"score_min": {
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"type": "string",
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"description": "Min acceptable alignment score w/r/t read length.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"L,-0.6,-0.6\"`. "
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}
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}
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},
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"reporting options": {
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"title": "Reporting Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"k": {
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"type": "integer",
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"description": "Report up to <int> alns per read; MAPQ not meaningful.",
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"help_text": "Type: `integer`, multiple: `False`, example: `10`. "
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},
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"all": {
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"type": "boolean",
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"description": "Report all alignments; very slow, MAPQ not meaningful.",
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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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"effort options": {
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"title": "Effort Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"D": {
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"type": "integer",
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"description": "Give up extending after <int> failed extends in a row.",
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"help_text": "Type: `integer`, multiple: `False`, example: `15`. "
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},
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"R": {
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"type": "integer",
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"description": "For reads w/ repetitive seeds, try <int> sets of seeds.",
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"help_text": "Type: `integer`, multiple: `False`, example: `2`. "
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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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"minins": {
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"type": "integer",
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"description": "Minimum fragment length.",
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"help_text": "Type: `integer`, multiple: `False`, example: `0`. "
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},
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"maxins": {
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"type": "integer",
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"description": "Maximum fragment length.",
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"help_text": "Type: `integer`, multiple: `False`, example: `500`. "
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},
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"fr": {
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"type": "boolean",
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"description": "-1, -2 mates align fw/rev (default).",
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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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"rf": {
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"type": "boolean",
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"description": "-1, -2 mates align rev/fw.",
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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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"ff": {
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"type": "boolean",
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"description": "-1, -2 mates align fw/fw.",
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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_mixed": {
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"type": "boolean",
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"description": "Suppress unpaired alignments for paired 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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"no_discordant": {
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"type": "boolean",
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"description": "Suppress discordant alignments for paired reads.",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"dovetail": {
|
|
"type": "boolean",
|
|
"description": "Concordant when mates extend past each other.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"no_contain": {
|
|
"type": "boolean",
|
|
"description": "Not concordant when one mate alignment contains other.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"no_overlap": {
|
|
"type": "boolean",
|
|
"description": "Not concordant when mates overlap at all.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"sam output options": {
|
|
"title": "SAM Output Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"time": {
|
|
"type": "boolean",
|
|
"description": "Print wall-clock time taken by search phases.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"quiet": {
|
|
"type": "boolean",
|
|
"description": "Print nothing to stderr except serious errors.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"met_stderr": {
|
|
"type": "boolean",
|
|
"description": "Send metrics to stderr.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"met": {
|
|
"type": "integer",
|
|
"description": "Report internal counters & metrics every <int> secs.",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
|
|
},
|
|
"no_unal": {
|
|
"type": "boolean",
|
|
"description": "Suppress SAM records for unaligned reads.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"no_head": {
|
|
"type": "boolean",
|
|
"description": "Suppress header lines, i.e",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"no_sq": {
|
|
"type": "boolean",
|
|
"description": "Suppress @SQ header lines.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"rg_id": {
|
|
"type": "string",
|
|
"description": "Set read group id, reflected in @RG line and RG:Z: opt field.",
|
|
"help_text": "Type: `string`, multiple: `False`, example: `\"sample1\"`. "
|
|
},
|
|
"rg": {
|
|
"type": "string",
|
|
"description": "Add <text> (\"lab:value\") to @RG line of SAM header.",
|
|
"help_text": "Type: `string`, multiple: `False`, example: `\"SM:sample1\"`. "
|
|
},
|
|
"omit_sec_seq": {
|
|
"type": "boolean",
|
|
"description": "Put '*' in SEQ and QUAL fields for secondary alignments.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sam_no_qname_trunc": {
|
|
"type": "boolean",
|
|
"description": "Suppress standard behavior of truncating readname at first whitespace.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"xeq": {
|
|
"type": "boolean",
|
|
"description": "Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"soft_clipped_unmapped_tlen": {
|
|
"type": "boolean",
|
|
"description": "Exclude soft-clipped bases when reporting TLEN.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sam_append_comment": {
|
|
"type": "boolean",
|
|
"description": "Append FASTA/FASTQ comment to SAM record.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"sam_opt_config": {
|
|
"type": "string",
|
|
"description": "Use config to toggle SAM Optional fields",
|
|
"help_text": "Type: `string`, multiple: `False`, example: `\"-MD,YP,-AS\"`. "
|
|
}
|
|
}
|
|
},
|
|
"bam options": {
|
|
"title": "BAM Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"align_paired_reads": {
|
|
"type": "boolean",
|
|
"description": "Align paired-end reads instead of unpaired BAM reads.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"preserve_tags": {
|
|
"type": "boolean",
|
|
"description": "Preserve tags from the original BAM record.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"performance options": {
|
|
"title": "Performance Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"reorder": {
|
|
"type": "boolean",
|
|
"description": "Force SAM output order to match order of input reads.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"mm": {
|
|
"type": "boolean",
|
|
"description": "Use memory-mapped I/O for index; many 'bowtie's can share.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"other options": {
|
|
"title": "Other Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"qc_filter": {
|
|
"type": "boolean",
|
|
"description": "Filter out reads that are bad according to QSEQ filter.",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
},
|
|
"seed": {
|
|
"type": "integer",
|
|
"description": "Seed for random number generator.",
|
|
"help_text": "Type: `integer`, multiple: `False`, example: `42`. "
|
|
},
|
|
"non_deterministic": {
|
|
"type": "boolean",
|
|
"description": "Seed rand",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"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/inputs"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/outputs"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/input format options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/alignment presets"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/alignment options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/scoring options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/reporting options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/effort options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/paired-end options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/sam output options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/bam options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/performance options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/other options"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|