{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "post_processing",
"description": "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "id": {
                "type":
                "string",
                "description": "Type: `string`, required, example: `foo`. ID of the sample",
                "help_text": "Type: `string`, required, example: `foo`. ID of the sample."
            
            }
    

        ,
                "strandedness": {
                "type":
                "string",
                "description": "Type: `string`, default: `auto`. Sample strand-specificity",
                "help_text": "Type: `string`, default: `auto`. Sample strand-specificity. Must be one of unstranded, forward, reverse or auto"
            ,
                "default": "auto"
            }
    

        ,
                "paired": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Paired fastq files or not?",
                "help_text": "Type: `boolean`. Paired fastq files or not?"
            
            }
    

        ,
                "fasta": {
                "type":
                "string",
                "description": "Type: `file`, required. Path to FASTA genome file",
                "help_text": "Type: `file`, required. Path to FASTA genome file."
            
            }
    

        ,
                "fai": {
                "type":
                "string",
                "description": "Type: `file`, required. Path to FASTA index",
                "help_text": "Type: `file`, required. Path to FASTA index"
            
            }
    

        ,
                "gtf": {
                "type":
                "string",
                "description": "Type: `file`. GTF file",
                "help_text": "Type: `file`. GTF file"
            
            }
    

        ,
                "genome_bam": {
                "type":
                "string",
                "description": "Type: `file`. Genome BAM file",
                "help_text": "Type: `file`. Genome BAM file"
            
            }
    

        ,
                "chrom_sizes": {
                "type":
                "string",
                "description": "Type: `file`. File containing chromosome lengths",
                "help_text": "Type: `file`. File containing chromosome lengths"
            
            }
    

        ,
                "star_multiqc": {
                "type":
                "string",
                "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."
            
            }
    

        ,
                "with_umi": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication",
                "help_text": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication."
            ,
                "default": "False"
            }
    

        ,
                "skip_qc": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

        ,
                "skip_markduplicates": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

        ,
                "skip_stringtie": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

        ,
                "skip_bigwig": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "processed_genome_bam": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. ",
                "help_text": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. "
            ,
                "default": "$id.$key.processed_genome_bam.bam"
            }
    

        ,
                "genome_bam_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ",
                "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. "
            ,
                "default": "$id.$key.genome_bam_index.bai"
            }
    

        ,
                "genome_bam_stats": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ",
                "help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. "
            ,
                "default": "$id.$key.genome_bam_stats.stats"
            }
    

        ,
                "genome_bam_flagstat": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ",
                "help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. "
            ,
                "default": "$id.$key.genome_bam_flagstat.flagstat"
            }
    

        ,
                "genome_bam_idxstats": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ",
                "help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. "
            ,
                "default": "$id.$key.genome_bam_idxstats.idxstats"
            }
    

        ,
                "markduplicates_metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. ",
                "help_text": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. "
            ,
                "default": "$id.$key.markduplicates_metrics.txt"
            }
    

        ,
                "stringtie_transcript_gtf": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. ",
                "help_text": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. "
            ,
                "default": "$id.$key.stringtie_transcript_gtf.gtf"
            }
    

        ,
                "stringtie_coverage_gtf": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. ",
                "help_text": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. "
            ,
                "default": "$id.$key.stringtie_coverage_gtf.gtf"
            }
    

        ,
                "stringtie_abundance": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. ",
                "help_text": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. "
            ,
                "default": "$id.$key.stringtie_abundance.txt"
            }
    

        ,
                "stringtie_ballgown": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. ",
                "help_text": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. "
            ,
                "default": "$id.$key.stringtie_ballgown.ballgown"
            }
    

        ,
                "bedgraph_forward": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ",
                "help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. "
            ,
                "default": "$id.$key.bedgraph_forward.bedgraph"
            }
    

        ,
                "bedgraph_reverse": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ",
                "help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. "
            ,
                "default": "$id.$key.bedgraph_reverse.bedgraph"
            }
    

        ,
                "bigwig_forward": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. ",
                "help_text": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. "
            ,
                "default": "$id.$key.bigwig_forward.bigwig"
            }
    

        ,
                "bigwig_reverse": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. ",
                "help_text": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. "
            ,
                "default": "$id.$key.bigwig_reverse.bigwig"
            }
    

}
},
    
    
    "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/input"
    },

    {
    "$ref": "#/definitions/output"
    },

    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }
]
}
