CI
e12b668142
Build pipeline: viash-hub.biobox.bump-viash-0-9-4-275jj
Source commit: be1cd83dd6
Source message: Add PR number
320 lines
12 KiB
JSON
320 lines
12 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "samtools_stats",
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"description": "Reports alignment summary statistics for a BAM file.",
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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 file",
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"help_text": "Type: `file`, required. Input file.\n"
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}
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,
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"bai": {
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"type":
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"string",
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"description": "Type: `file`. Index file",
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"help_text": "Type: `file`. Index file.\n"
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}
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,
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"fasta": {
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"type":
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"string",
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"description": "Type: `file`. Reference file the CRAM was created with",
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"help_text": "Type: `file`. Reference file the CRAM was created with.\n"
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}
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,
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"coverage": {
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"type":
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"string",
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"description": "Type: List of `integer`, example: `1;1000;1`, multiple_sep: `\";\"`. Coverage distribution min;max;step",
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"help_text": "Type: List of `integer`, example: `1;1000;1`, multiple_sep: `\";\"`. Coverage distribution min;max;step. Default: [1, 1000, 1].\n"
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}
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,
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"remove_dups": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Exclude from statistics reads marked as duplicates",
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"help_text": "Type: `boolean_true`, default: `false`. Exclude from statistics reads marked as duplicates.\n"
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,
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"default":false
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}
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,
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"customized_index_file": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use a customized index file",
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"help_text": "Type: `boolean_true`, default: `false`. Use a customized index file.\n"
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,
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"default":false
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}
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,
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"required_flag": {
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"type":
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"string",
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"description": "Type: `string`, example: `0`. Required flag, 0 for unset",
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"help_text": "Type: `string`, example: `0`. Required flag, 0 for unset. See also `samtools flags`. Default: `\"0\"`.\n"
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}
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,
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"filtering_flag": {
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"type":
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"string",
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"description": "Type: `string`, example: `0`. Filtering flag, 0 for unset",
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"help_text": "Type: `string`, example: `0`. Filtering flag, 0 for unset. See also `samtools flags`. Default: `0`.\n"
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}
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,
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"GC_depth": {
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"type":
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"number",
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"description": "Type: `double`, example: `20000.0`. The size of GC-depth bins (decreasing bin size increases memory requirement)",
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"help_text": "Type: `double`, example: `20000.0`. The size of GC-depth bins (decreasing bin size increases memory requirement). Default: `20000`.\n"
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}
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,
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"insert_size": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `8000`. Maximum insert size",
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"help_text": "Type: `integer`, example: `8000`. Maximum insert size. Default: `8000`.\n"
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}
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,
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"id": {
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"type":
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"string",
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"description": "Type: `string`. Include only listed read group or sample name",
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"help_text": "Type: `string`. Include only listed read group or sample name.\n"
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}
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,
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"read_length": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `-1`. Include in the statistics only reads with the given read length",
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"help_text": "Type: `integer`, example: `-1`. Include in the statistics only reads with the given read length. Default: `-1`.\n"
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}
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,
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"most_inserts": {
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"type":
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"number",
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"description": "Type: `double`, example: `0.99`. Report only the main part of inserts",
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"help_text": "Type: `double`, example: `0.99`. Report only the main part of inserts. Default: `0.99`.\n"
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}
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,
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"split_prefix": {
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"type":
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"string",
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"description": "Type: `string`. Path or string prefix for filepaths output by --split (default is input filename)",
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"help_text": "Type: `string`. Path or string prefix for filepaths output by --split (default is input filename).\n"
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}
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,
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"trim_quality": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `0`. The BWA trimming parameter",
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"help_text": "Type: `integer`, example: `0`. The BWA trimming parameter. Default: `0`.\n"
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}
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,
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"ref_seq": {
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"type":
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"string",
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"description": "Type: `file`. Reference sequence (required for GC-depth and mismatches-per-cycle calculation)",
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"help_text": "Type: `file`. Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n"
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}
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,
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"split": {
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"type":
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"string",
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"description": "Type: `string`. Also write statistics to separate files split by tagged field",
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"help_text": "Type: `string`. Also write statistics to separate files split by tagged field.\n"
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}
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,
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"target_regions": {
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"type":
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"string",
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"description": "Type: `file`. Do stats in these regions only",
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"help_text": "Type: `file`. Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n"
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}
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,
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"sparse": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Suppress outputting IS rows where there are no insertions",
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"help_text": "Type: `boolean_true`, default: `false`. Suppress outputting IS rows where there are no insertions.\n"
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,
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"default":false
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}
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,
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"remove_overlaps": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Remove overlaps of paired-end reads from coverage and base count computations",
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"help_text": "Type: `boolean_true`, default: `false`. Remove overlaps of paired-end reads from coverage and base count computations.\n"
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,
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"default":false
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}
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,
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"cov_threshold": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `0`. Only bases with coverage above this value will be included in the target percentage computation",
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"help_text": "Type: `integer`, example: `0`. Only bases with coverage above this value will be included in the target percentage computation. Default: `0`.\n"
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}
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,
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"input_fmt_option": {
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"type":
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"string",
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"description": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE",
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"help_text": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE.\n"
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}
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,
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"reference": {
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"type":
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"string",
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"description": "Type: `file`. Reference sequence FASTA FILE",
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"help_text": "Type: `file`. Reference sequence FASTA FILE.\n"
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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.$key.output.txt`, example: `out.txt`. Output file",
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"help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `out.txt`. Output file.\n"
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,
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"default":"$id.$key.output.txt"
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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/nextflow input-output arguments"
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}
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]
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}
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