"description":"Type: `file`. STAR align log file",
"help_text":"Type: `file`. STAR align log file."
}
,
"extra_picard_args":{
"type":
"string",
"description":"Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline",
"help_text":"Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline."
,
"default":""
}
,
"extra_stringtie_args":{
"type":
"string",
"description":"Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline",
"help_text":"Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline."
,
"default":""
}
,
"stringtie_ignore_gtf":{
"type":
"boolean",
"description":"Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i",
"help_text":"Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don\u0027t restrict to those in GTF file."
}
,
"extra_bedtools_args":{
"type":
"string",
"description":"Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline",
"help_text":"Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline."
,
"default":""
}
,
"bam_csi_index":{
"type":
"boolean",
"description":"Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index",
"help_text":"Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes."
,
"default":"False"
}
,
"min_mapped_reads":{
"type":
"integer",
"description":"Type: `integer`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing",
"help_text":"Type: `integer`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing."
"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.",
