CI
56a195f1bb
Build pipeline: vsh-ci-template-bbg2t
Source commit: d97e3156fe
Source message: Rename biobase -> biobox
356 lines
16 KiB
JSON
356 lines
16 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "samtools_fastq",
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"description": "Converts a SAM, BAM or CRAM to FASTQ format.",
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"type": "object",
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"definitions": {
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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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"input": {
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"type":
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"string",
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"description": "Type: `file`, required. input SAM/BAM/CRAM file",
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"help_text": "Type: `file`, required. input SAM/BAM/CRAM file"
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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":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file",
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"help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file"
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,
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"default": "$id.$key.output.output"
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}
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}
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},
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"options" : {
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"title": "Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"no_suffix": {
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"type":
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"boolean",
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"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",
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"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"
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,
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"default": "False"
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}
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,
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"suffix": {
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"type":
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"boolean",
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"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",
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"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"
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,
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"default": "False"
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}
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,
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"use_oq": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available",
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"help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n"
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,
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"default": "False"
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}
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,
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"singleton": {
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"type":
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"string",
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"description": "Type: `file`. write singleton reads to FILE",
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"help_text": "Type: `file`. write singleton reads to FILE."
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}
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,
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"copy_tags": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist",
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"help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n"
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,
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"default": "False"
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}
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,
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"copy_tags_list": {
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"type":
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"string",
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"description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist",
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"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"
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}
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,
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"read1": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them",
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"help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n"
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,
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"default": "$id.$key.read1.read1"
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}
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,
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"read2": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them",
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"help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n"
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,
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"default": "$id.$key.read2.read2"
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}
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,
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"output_reads": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout",
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"help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n"
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,
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"default": "$id.$key.output_reads.output_reads"
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}
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,
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"output_reads_both": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them",
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"help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n"
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,
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"default": "$id.$key.output_reads_both.output_reads_both"
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}
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,
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"filter_flags": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `0`. Only output alignments with all bits set in INT present in the FLAG field",
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"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"
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,
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"default": "0"
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}
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,
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"excl_flags": {
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"type":
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"string",
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"description": "Type: `string`, default: `2304`. Do not output alignments with any bits set in INT present in the FLAG field",
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"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"
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,
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"default": "2304"
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}
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,
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"incl_flags": {
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"type":
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"string",
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"description": "Type: `string`, default: `0`. Only output alignments with any bits set in INT present in the FLAG field",
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"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"
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,
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"default": "0"
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}
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,
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"excl_flags_all": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field",
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"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"
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,
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"default": "0"
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}
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,
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"aux_tag": {
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"type":
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"string",
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"description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL",
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"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"
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}
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,
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"aux_tag_file": {
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"type":
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"string",
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"description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE",
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"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"
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}
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,
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"casava": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. add Illumina Casava 1",
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"help_text": "Type: `boolean_true`, default: `false`. add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
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,
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"default": "False"
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}
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,
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"compression": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files",
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"help_text": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files."
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,
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"default": "0"
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}
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,
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"index1": {
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"type":
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"string",
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"description": "Type: `file`. write first index reads to FILE",
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"help_text": "Type: `file`. write first index reads to FILE."
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}
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,
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"index2": {
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"type":
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"string",
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"description": "Type: `file`. write second index reads to FILE",
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"help_text": "Type: `file`. write second index reads to FILE."
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}
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,
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"barcode_tag": {
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"type":
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"string",
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"description": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in",
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"help_text": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in."
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,
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"default": "BC"
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}
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,
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"quality_tag": {
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"type":
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"string",
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"description": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in",
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"help_text": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in."
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,
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"default": "QT"
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}
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,
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"index_format": {
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"type":
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"string",
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"description": "Type: `string`. string to describe how to parse the barcode and quality tags",
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"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"
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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":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"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.",
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"hidden": true
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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": "#/definitions/inputs"
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},
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{
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"$ref": "#/definitions/outputs"
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},
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{
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"$ref": "#/definitions/options"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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