CI
18d6cad4c4
Build pipeline: viash-hub.biobox.main-bjgnf
Source commit: 2b29a47575
Source message: Bedtools GroupBY (#123)
* Initial Commit
* Update config.vsh.yaml
* config file
* script.sh
* adding some tests
* more test
* Update CHANGELOG.md
* deleted test_data
* bug fix
* Update config.vsh.yaml
* adding more links
* exit on error
* $TMPDIR
* Update script.sh
* Update config.vsh.yaml
* Suggested change on column option
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
776 lines
33 KiB
JSON
776 lines
33 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/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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"definitions": {
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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":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n"
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}
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,
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"front": {
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"type":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n"
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}
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,
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"anywhere": {
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"type":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n"
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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":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\";\"`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: List of `file`, multiple_sep: `\";\"`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n"
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}
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,
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"front_fasta": {
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"type":
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"string",
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"description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n"
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}
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,
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"anywhere_fasta": {
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"type":
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"string",
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"description": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)",
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"help_text": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n"
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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":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n"
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}
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,
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"front_r2": {
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"type":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n"
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}
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,
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"anywhere_r2": {
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"type":
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"string",
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"description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)",
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"help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n"
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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":
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"string",
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"description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n"
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}
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,
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"front_r2_fasta": {
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"type":
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"string",
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"description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)",
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"help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n"
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}
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,
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"anywhere_r2_fasta": {
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"type":
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"string",
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"description": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)",
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"help_text": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n"
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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":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Treat adapters given with -a/-A etc",
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"help_text": "Type: `boolean_true`, default: `false`. Treat adapters given with -a/-A etc. as pairs. Either both\nor none are removed from each read pair.\n"
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,
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"default": "False"
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}
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,
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"pair_filter": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``any`, `both`, `first``. Which of the reads in a paired-end read have to match the\nfiltering criterion in order for the pair to be filtered",
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"help_text": "Type: `string`, choices: ``any`, `both`, `first``. 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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"enum": ["any", "both", "first"]
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}
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,
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"interleaved": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Read and/or write interleaved paired-end reads",
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"help_text": "Type: `boolean_true`, default: `false`. Read and/or write interleaved paired-end reads.\n"
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,
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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":
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"string",
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"description": "Type: `file`, required. Input fastq file for single-end reads or R1 for paired-end reads",
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"help_text": "Type: `file`, required. Input fastq file for single-end reads or R1 for paired-end reads.\n"
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}
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,
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"input_r2": {
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"type":
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"string",
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"description": "Type: `file`. Input fastq file for R2 in the case of paired-end reads",
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"help_text": "Type: `file`. Input fastq file for R2 in the case of paired-end reads.\n"
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}
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,
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"error_rate": {
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"type":
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"number",
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"description": "Type: `double`, example: `0.1`. Maximum allowed error rate (if 0 \u003c= E \u003c 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger \u003e= 1)",
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"help_text": "Type: `double`, example: `0.1`. Maximum allowed error rate (if 0 \u003c= E \u003c 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger \u003e= 1). Error rate = no. of errors divided by\nlength of matching region. Default: 0.1 (10%).\n"
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}
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,
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"no_indels": {
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"type":
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"boolean",
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"description": "Type: `boolean_false`, default: `true`. Allow only mismatches in alignments",
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"help_text": "Type: `boolean_false`, default: `true`. Allow only mismatches in alignments.\n"
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,
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"default": "True"
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}
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,
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"times": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `1`. Remove up to COUNT adapters from each read",
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"help_text": "Type: `integer`, example: `1`. Remove up to COUNT adapters from each read. Default: 1.\n"
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}
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,
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"overlap": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `3`. Require MINLENGTH overlap between read and adapter for an\nadapter to be found",
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"help_text": "Type: `integer`, example: `3`. Require MINLENGTH overlap between read and adapter for an\nadapter to be found. The default is 3.\n"
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}
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,
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"match_read_wildcards": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Interpret IUPAC wildcards in reads",
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"help_text": "Type: `boolean_true`, default: `false`. Interpret IUPAC wildcards in reads.\n"
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,
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"default": "False"
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}
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,
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"no_match_adapter_wildcards": {
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"type":
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"boolean",
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"description": "Type: `boolean_false`, default: `true`. Do not interpret IUPAC wildcards in adapters",
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"help_text": "Type: `boolean_false`, default: `true`. Do not interpret IUPAC wildcards in adapters.\n"
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,
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"default": "True"
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}
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,
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"action": {
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"type":
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"string",
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"description": "Type: `string`, example: `trim`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. What to do if a match was found",
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"help_text": "Type: `string`, example: `trim`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. What to do if a match was found. trim: trim adapter and\nup- or downstream sequence; retain: trim, but retain\nadapter; mask: replace with \u0027N\u0027 characters; lowercase:\nconvert to lowercase; none: leave unchanged.\nThe default is trim.\n",
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"enum": ["trim", "retain", "mask", "lowercase", "none"]
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}
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,
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"revcomp": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Check both the read and its reverse complement for adapter\nmatches",
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"help_text": "Type: `boolean_true`, default: `false`. Check both the read and its reverse complement for adapter\nmatches. If match is on reverse-complemented version,\noutput that one.\n"
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,
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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":
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"string",
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"description": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it",
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"help_text": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it.\nWith mode \u0027unique_dual\u0027, adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode \u0027combinatorial_dual\u0027 allows all combinations of the sets of indexes\non R1 and R2. It is necessary to write each read pair to an output\nfile depending on the adapters found on both R1 and R2.\nMode \u0027single\u0027, uses indexes or barcodes located at the 5\u0027\nend of the R1 read (single). \n",
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"enum": ["single", "unique_dual", "combinatorial_dual"]
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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":
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"string",
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"description": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2)",
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"help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2). If LEN is positive, remove bases from the\nbeginning. If LEN is negative, remove bases from the end.\nCan be used twice if LENs have different signs. Applied\n*before* adapter trimming.\n"
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}
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,
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"cut_r2": {
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"type":
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"string",
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"description": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (for R2)",
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"help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (for R2). If LEN is positive, remove bases from the\nbeginning. If LEN is negative, remove bases from the end.\nCan be used twice if LENs have different signs. Applied\n*before* adapter trimming.\n"
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}
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,
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"nextseq_trim": {
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"type":
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"string",
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"description": "Type: `string`. NextSeq-specific quality trimming (each read)",
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"help_text": "Type: `string`. NextSeq-specific quality trimming (each read). Trims also\ndark cycles appearing as high-quality G bases.\n"
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}
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,
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"quality_cutoff": {
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"type":
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"string",
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"description": "Type: `string`. Trim low-quality bases from 5\u0027 and/or 3\u0027 ends of each read\nbefore adapter removal",
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"help_text": "Type: `string`. Trim low-quality bases from 5\u0027 and/or 3\u0027 ends of each read\nbefore adapter removal. Applied to both reads if data is\npaired. If one value is given, only the 3\u0027 end is trimmed.\nIf two comma-separated cutoffs are given, the 5\u0027 end is\ntrimmed with the first cutoff, the 3\u0027 end with the second.\n"
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}
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,
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"quality_cutoff_r2": {
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"type":
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"string",
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"description": "Type: `string`. Quality-trimming cutoff for R2",
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"help_text": "Type: `string`. Quality-trimming cutoff for R2. Default: same as for R1\n"
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}
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,
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"quality_base": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `33`. Assume that quality values in FASTQ are encoded as\nascii(quality + N)",
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"help_text": "Type: `integer`, example: `33`. Assume that quality values in FASTQ are encoded as\nascii(quality + N). This needs to be set to 64 for some\nold Illumina FASTQ files. The default is 33.\n"
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}
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,
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"poly_a": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Trim poly-A tails",
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"help_text": "Type: `boolean_true`, default: `false`. Trim poly-A tails"
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,
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"default": "False"
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}
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,
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"length": {
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"type":
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"integer",
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"description": "Type: `integer`. Shorten reads to LENGTH",
|
|
"help_text": "Type: `integer`. Shorten reads to LENGTH. Positive values remove bases at\nthe end while negative ones remove bases at the beginning.\nThis and the following modifications are applied after\nadapter trimming.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"trim_n": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Trim N\u0027s on ends of reads",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Trim N\u0027s on ends of reads."
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"length_tag": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `length=`. Search for TAG followed by a decimal number in the\ndescription field of the read",
|
|
"help_text": "Type: `string`, example: `length=`. Search for TAG followed by a decimal number in the\ndescription field of the read. Replace the decimal number\nwith the correct length of the trimmed read. For example,\nuse --length-tag \u0027length=\u0027 to correct fields like\n\u0027length=123\u0027.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"strip_suffix": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Remove this suffix from read names if present",
|
|
"help_text": "Type: `string`. Remove this suffix from read names if present. Can be\ngiven multiple times.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"prefix": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Add this prefix to read names",
|
|
"help_text": "Type: `string`. Add this prefix to read names. Use {name} to insert the\nname of the matching adapter.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"suffix": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Add this suffix to read names; can also include {name}\n",
|
|
"help_text": "Type: `string`. Add this suffix to read names; can also include {name}\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"rename": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc",
|
|
"help_text": "Type: `string`. Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc. (see documentation)\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"zero_cap": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Change negative quality values to zero",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Change negative quality values to zero."
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"filtering of processed reads" : {
|
|
"title": "Filtering of processed reads",
|
|
"type": "object",
|
|
"description": "Filters are applied after above read modifications. Paired-end reads are\nalways discarded pairwise (see also --pair_filter).\n",
|
|
"properties": {
|
|
|
|
|
|
"minimum_length": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `0`. Discard reads shorter than LEN",
|
|
"help_text": "Type: `string`, example: `0`. Discard reads shorter than LEN. Default is 0.\nWhen trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately by separating them with a colon (:).\nIf the colon syntax is not used, the same minimum length applies to both reads, as discussed above.\nAlso, one of the values can be omitted to impose no restrictions.\nFor example, with -m 17:, the length of R1 must be at least 17, but the length of R2 is ignored.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"maximum_length": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Discard reads longer than LEN",
|
|
"help_text": "Type: `string`. Discard reads longer than LEN. Default: no limit.\nFor paired reads, see the remark for --minimum_length\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"max_n": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Discard reads with more than COUNT \u0027N\u0027 bases",
|
|
"help_text": "Type: `string`. Discard reads with more than COUNT \u0027N\u0027 bases. If COUNT is\na number between 0 and 1, it is interpreted as a fraction\nof the read length.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"max_expected_errors": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `long`. Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS",
|
|
"help_text": "Type: `long`. Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"max_average_error_rate": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `long`. as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length",
|
|
"help_text": "Type: `long`. as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"discard_trimmed": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Discard reads that contain an adapter",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Discard reads that contain an adapter. Use also -O to\navoid discarding too many randomly matching reads.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"discard_untrimmed": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Discard reads that do not contain an adapter",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Discard reads that do not contain an adapter.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"discard_casava": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Discard reads that did not pass CASAVA filtering (header\nhas :Y:)",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Discard reads that did not pass CASAVA filtering (header\nhas :Y:).\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"output parameters" : {
|
|
"title": "Output parameters",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"report": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `full`, choices: ``full`, `minimal``. Which type of report to print: \u0027full\u0027 (default) or \u0027minimal\u0027",
|
|
"help_text": "Type: `string`, example: `full`, choices: ``full`, `minimal``. Which type of report to print: \u0027full\u0027 (default) or \u0027minimal\u0027.\n",
|
|
"enum": ["full", "minimal"]
|
|
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"json": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Write report in JSON format to this file",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Write report in JSON format to this file.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: List of `file`, required, default: `$id.$key.output_*.fast[a,q]`, example: `fastq/*_001.fast[a,q]`, multiple_sep: `\";\"`. Glob pattern for matching the expected output files",
|
|
"help_text": "Type: List of `file`, required, default: `$id.$key.output_*.fast[a,q]`, example: `fastq/*_001.fast[a,q]`, multiple_sep: `\";\"`. Glob pattern for matching the expected output files.\nShould include `$output_dir`.\n"
|
|
,
|
|
"default": "$id.$key.output_*.fast[a,q]"
|
|
}
|
|
|
|
|
|
,
|
|
"fasta": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Output FASTA to standard output even on FASTQ input",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Output FASTA to standard output even on FASTQ input.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"info_file": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Write information about each read and its adapter matches\ninto info",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Write information about each read and its adapter matches\ninto info.txt in the output directory.\nSee the documentation for the file format.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"debug" : {
|
|
"title": "Debug",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"debug": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Print debug information",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Print debug information"
|
|
,
|
|
"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": "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/specify adapters for r1"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/specify adapters using fasta files for r1"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/specify adapters for r2"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/specify adapters using fasta files for r2"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/paired-end options"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/input parameters"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/demultiplexing options"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/read modifications"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/filtering of processed reads"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/output parameters"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/debug"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|