{ "$schema": "http://json-schema.org/draft-07/schema", "title": "samtools_fastq", "description": "Converts a SAM, BAM or CRAM to FASTQ format.", "type": "object", "definitions": { "inputs" : { "title": "Inputs", "type": "object", "description": "No description", "properties": { "input": { "type": "string", "description": "Type: `file`, required. input SAM/BAM/CRAM file", "help_text": "Type: `file`, required. input SAM/BAM/CRAM file" } } }, "outputs" : { "title": "Outputs", "type": "object", "description": "No description", "properties": { "output": { "type": "string", "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file" , "default": "$id.$key.output.output" } } }, "options" : { "title": "Options", "type": "object", "description": "No description", "properties": { "no_suffix": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", "help_text": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.\n" , "default": "False" } , "suffix": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files", "help_text": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files.\n" , "default": "False" } , "use_oq": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available", "help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n" , "default": "False" } , "singleton": { "type": "string", "description": "Type: `file`. write singleton reads to FILE", "help_text": "Type: `file`. write singleton reads to FILE." } , "copy_tags": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist", "help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n" , "default": "False" } , "copy_tags_list": { "type": "string", "description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist", "help_text": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. \nTAGLIST can be blank or * to indicate all tags should be copied to the output. If using *, \nbe careful to quote it to avoid unwanted shell expansion.\n" } , "read1": { "type": "string", "description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", "help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , "default": "$id.$key.read1.read1" } , "read2": { "type": "string", "description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", "help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , "default": "$id.$key.read2.read2" } , "output_reads": { "type": "string", "description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", "help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" , "default": "$id.$key.output_reads.output_reads" } , "output_reads_both": { "type": "string", "description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", "help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" , "default": "$id.$key.output_reads_both.output_reads_both" } , "filter_flags": { "type": "integer", "description": "Type: `integer`, default: `0`. Only output alignments with all bits set in INT present in the FLAG field", "help_text": "Type: `integer`, default: `0`. Only output alignments with all bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/).\n" , "default": "0" } , "excl_flags": { "type": "string", "description": "Type: `string`, default: `2304`. Do not output alignments with any bits set in INT present in the FLAG field", "help_text": "Type: `string`, default: `2304`. Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and \nsupplementary alignments.\n" , "default": "2304" } , "incl_flags": { "type": "string", "description": "Type: `string`, default: `0`. Only output alignments with any bits set in INT present in the FLAG field", "help_text": "Type: `string`, default: `0`. Only output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of \nflag names.\n" , "default": "0" } , "excl_flags_all": { "type": "integer", "description": "Type: `integer`, default: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", "help_text": "Type: `integer`, default: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/).\n" , "default": "0" } , "aux_tag": { "type": "string", "description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL", "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is comparable to the method used in samtools view --tag. The option may be specified \nmultiple times and is equivalent to using the --aux_tag_file option.\n" } , "aux_tag_file": { "type": "string", "description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. \nThe format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.\n" } , "casava": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. add Illumina Casava 1", "help_text": "Type: `boolean_true`, default: `false`. add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" , "default": "False" } , "compression": { "type": "integer", "description": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files", "help_text": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files." , "default": "0" } , "index1": { "type": "string", "description": "Type: `file`. write first index reads to FILE", "help_text": "Type: `file`. write first index reads to FILE." } , "index2": { "type": "string", "description": "Type: `file`. write second index reads to FILE", "help_text": "Type: `file`. write second index reads to FILE." } , "barcode_tag": { "type": "string", "description": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in", "help_text": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in." , "default": "BC" } , "quality_tag": { "type": "string", "description": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in", "help_text": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in." , "default": "QT" } , "index_format": { "type": "string", "description": "Type: `string`. string to describe how to parse the barcode and quality tags", "help_text": "Type: `string`. string to describe how to parse the barcode and quality tags. For example:\n[i14i8]: the first 14 characters are index 1, the next 8 characters are index 2.\n[n8i14]: ignore the first 8 characters, and use the next 14 characters for index 1.\nIf the tag contains a separator, then the numeric part can be replaced with \u0027*\u0027 to mean \n\u0027read until the separator or end of tag\u0027, for example: [n*i*].\n" } } }, "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": "Type: `string`, required, example: `output/`. Path to an output directory", "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." } , "param_list": { "type": "string", "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", "hidden": true } } } }, "allOf": [ { "$ref": "#/definitions/inputs" }, { "$ref": "#/definitions/outputs" }, { "$ref": "#/definitions/options" }, { "$ref": "#/definitions/nextflow input-output arguments" } ] }