{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "quality_control",
"description": "A subworkflow for the final quality control stage of the 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: `test`. ID of the sample",
                "help_text": "Type: `string`, required, example: `test`. ID of the sample"
            
            }
    

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

        ,
                "paired": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Paired-end reads?",
                "help_text": "Type: `boolean`. Paired-end reads?"
            
            }
    

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

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

        ,
                "gene_bed": {
                "type":
                "string",
                "description": "Type: `file`. Path to BED file containing gene intervals",
                "help_text": "Type: `file`. Path to BED file containing gene intervals. This will be created from the GTF file if not specified."
            
            }
    

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

        ,
                "gtf_group_features": {
                "type":
                "string",
                "description": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon",
                "help_text": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon."
            ,
                "default": "gene_id"
            }
    

        ,
                "gtf_extra_attributes": {
                "type":
                "string",
                "description": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon",
                "help_text": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon."
            ,
                "default": "gene_name"
            }
    

        ,
                "quant_out_dir": {
                "type":
                "string",
                "description": "Type: `file`. Directory containing Salmon quantification results",
                "help_text": "Type: `file`. Directory containing Salmon quantification results."
            
            }
    

        ,
                "quant_results_file": {
                "type":
                "string",
                "description": "Type: `file`. Salmon quantification file",
                "help_text": "Type: `file`. Salmon quantification file."
            
            }
    

        ,
                "pseudo_quant_out_dir": {
                "type":
                "string",
                "description": "Type: `file`. Directory containing quantification results for pseudo alignment",
                "help_text": "Type: `file`. Directory containing quantification results for pseudo alignment."
            
            }
    

        ,
                "pseudo_salmon_quant_results_file": {
                "type":
                "string",
                "description": "Type: `file`. Quantification file from Salmon for pseudo alignment",
                "help_text": "Type: `file`. Quantification file from Salmon for pseudo alignment."
            
            }
    

        ,
                "pseudo_kallisto_quant_results_file": {
                "type":
                "string",
                "description": "Type: `file`. Quantification file from Kallisto for pseudo alignment",
                "help_text": "Type: `file`. Quantification file from Kallisto for pseudo alignment."
            
            }
    

        ,
                "aligner": {
                "type":
                "string",
                "description": "Type: `string`. Method used for alognment and qqunatification",
                "help_text": "Type: `string`. Method used for alognment and qqunatification."
            
            }
    

        ,
                "pseudo_aligner": {
                "type":
                "string",
                "description": "Type: `string`. Method used for pseudo alignment and quantification",
                "help_text": "Type: `string`. Method used for pseudo alignment and quantification."
            
            }
    

        ,
                "rsem_counts_gene": {
                "type":
                "string",
                "description": "Type: `file`. Expression counts on gene level",
                "help_text": "Type: `file`. Expression counts on gene level"
            
            }
    

        ,
                "rsem_counts_transcripts": {
                "type":
                "string",
                "description": "Type: `file`. Expression counts on transcript level",
                "help_text": "Type: `file`. Expression counts on transcript level"
            
            }
    

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

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

        ,
                "skip_align": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `false`. ",
                "help_text": "Type: `boolean`, default: `false`. "
            ,
                "default": "False"
            }
    

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

        ,
                "skip_preseq": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `false`. ",
                "help_text": "Type: `boolean`, default: `false`. "
            ,
                "default": "False"
            }
    

        ,
                "extra_preseq_args": {
                "type":
                "string",
                "description": "Type: `string`, default: `-verbose -bam -seed 1`. ",
                "help_text": "Type: `string`, default: `-verbose -bam -seed 1`. "
            ,
                "default": "-verbose -bam -seed 1"
            }
    

        ,
                "featurecounts_group_type": {
                "type":
                "string",
                "description": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts",
                "help_text": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts."
            ,
                "default": "gene_biotype"
            }
    

        ,
                "featurecounts_feature_type": {
                "type":
                "string",
                "description": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file",
                "help_text": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file."
            ,
                "default": "exon"
            }
    

        ,
                "gencode": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Specify if the GTF annotation is in GENCODE format",
                "help_text": "Type: `boolean`. Specify if the GTF annotation is in GENCODE format."
            
            }
    

        ,
                "biotypes_header": {
                "type":
                "string",
                "description": "Type: `file`, default: `assets/multiqc/biotypes_header.txt`. ",
                "help_text": "Type: `file`, default: `assets/multiqc/biotypes_header.txt`. "
            ,
                "default": "assets/multiqc/biotypes_header.txt"
            }
    

        ,
                "biotype": {
                "type":
                "string",
                "description": "Type: `string`. Biotype value to use while appending entries to GTF file when additional fasta file is provided",
                "help_text": "Type: `string`. Biotype value to use while appending entries to GTF file when additional fasta file is provided."
            
            }
    

        ,
                "extra_featurecounts_args": {
                "type":
                "string",
                "description": "Type: `string`. Extra arguments to pass to featureCounts command in addition to defaults defined by the pipeline",
                "help_text": "Type: `string`. Extra arguments to pass to featureCounts command in addition to defaults defined by the pipeline"
            
            }
    

        ,
                "rseqc_modules": {
                "type":
                "string",
                "description": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf",
                "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf",
                "enum": ["bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin"]
            
            ,
                "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
            }
    

        ,
                "sample_size": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file to infer experiment and calculate inner distance, default = 200000",
                "help_text": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file to infer experiment and calculate inner distance, default = 200000."
            ,
                "default": "200000"
            }
    

        ,
                "lower_bound_size": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp)",
                "help_text": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp). This option is used for ploting histograme, default = -250."
            ,
                "default": "-250"
            }
    

        ,
                "upper_bound_size": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `250`. Upper bound of inner distance (bp)",
                "help_text": "Type: `integer`, default: `250`. Upper bound of inner distance (bp). This option is used for ploting histograme, default = 250."
            ,
                "default": "250"
            }
    

        ,
                "step_size": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `5`. Step size (bp) of histograme of inner distance",
                "help_text": "Type: `integer`, default: `5`. Step size (bp) of histograme of inner distance. This option is used for plotting histogram, default = 5."
            ,
                "default": "5"
            }
    

        ,
                "map_qual": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default = 30",
                "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default = 30."
            ,
                "default": "30"
            }
    

        ,
                "min_intron": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `50`. Minimum intron length (bp) to call a junction, default = 50",
                "help_text": "Type: `integer`, default: `50`. Minimum intron length (bp) to call a junction, default = 50."
            ,
                "default": "50"
            }
    

        ,
                "min_splice_read": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1",
                "help_text": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1."
            ,
                "default": "1"
            }
    

        ,
                "sampling_percentile_lower_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `5`. Read sampling for junction saturation starts from this percentile, must be an integer between 0 and 100, default = 5",
                "help_text": "Type: `integer`, default: `5`. Read sampling for junction saturation starts from this percentile, must be an integer between 0 and 100, default = 5."
            ,
                "default": "5"
            }
    

        ,
                "sampling_percentile_upper_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `100`. Read sampling for junction saturation ends at this percentile, must be an integer between 0 and 100, default = 5",
                "help_text": "Type: `integer`, default: `100`. Read sampling for junction saturation ends at this percentile, must be an integer between 0 and 100, default = 5."
            ,
                "default": "100"
            }
    

        ,
                "sampling_percentile_step": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `5`. Read sampling for junction saturation frequency in %",
                "help_text": "Type: `integer`, default: `5`. Read sampling for junction saturation frequency in %. Smaller value means more sampling times. Must be an integer between 0 and 100, default = 5."
            ,
                "default": "5"
            }
    

        ,
                "read_count_upper_limit": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence to determine read duplication",
                "help_text": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence to determine read duplication. Only used for plotting, default = 500 (times)."
            ,
                "default": "500"
            }
    

        ,
                "minimum_coverage": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript to determin tin, default = 10",
                "help_text": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript to determin tin, default = 10."
            ,
                "default": "10"
            }
    

        ,
                "tin_sample_size": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA",
                "help_text": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA. Note, if this number is larger than the length of mRNA (L), it will be halved until it\u0027s smaller than L (default = 100)"
            ,
                "default": "100"
            }
    

        ,
                "subtract_background": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads) to determine tin",
                "help_text": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads) to determine tin. Only use this option if there are substantial intronic reads."
            ,
                "default": "False"
            }
    

        ,
                "output_format": {
                "type":
                "string",
                "description": "Type: `string`, default: `html`, choices: ``html`, `pdf``. Format of the qualimap output report (PDF or HTML, default is HTML)",
                "help_text": "Type: `string`, default: `html`, choices: ``html`, `pdf``. Format of the qualimap output report (PDF or HTML, default is HTML)",
                "enum": ["html", "pdf"]
            
            ,
                "default": "html"
            }
    

        ,
                "pr_bases": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias for qualimap (default = 100)",
                "help_text": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias for qualimap (default = 100)."
            ,
                "default": "100"
            }
    

        ,
                "tr_bias": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias for qualimap (default = 1000)",
                "help_text": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias for qualimap (default = 1000)."
            ,
                "default": "1000"
            }
    

        ,
                "algorithm": {
                "type":
                "string",
                "description": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm for qualimap (uniquely-mapped-reads (default) or proportional)",
                "help_text": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm for qualimap (uniquely-mapped-reads (default) or proportional)."
            ,
                "default": "uniquely-mapped-reads"
            }
    

        ,
                "sequencing_protocol": {
                "type":
                "string",
                "description": "Type: `string`, default: `non-strand-specific`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol for qualimap (strand-specific-forward, strand-specific-reverse or non-strand-specific (default))",
                "help_text": "Type: `string`, default: `non-strand-specific`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol for qualimap (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).",
                "enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"]
            
            ,
                "default": "non-strand-specific"
            }
    

        ,
                "sorted": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name",
                "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed for qualimap. Only requiredfor paired-end analysis."
            ,
                "default": "False"
            }
    

        ,
                "java_memory_size": {
                "type":
                "string",
                "description": "Type: `string`, default: `4G`. maximum Java heap memory size for qualimap, default = 4G",
                "help_text": "Type: `string`, default: `4G`. maximum Java heap memory size for qualimap, default = 4G."
            ,
                "default": "4G"
            }
    

        ,
                "skip_deseq2_qc": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

        ,
                "pca_header_multiqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. ",
                "help_text": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. "
            ,
                "default": "assets/multiqc/deseq2_pca_header.txt"
            }
    

        ,
                "clustering_header_multiqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. ",
                "help_text": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. "
            ,
                "default": "assets/multiqc/deseq2_clustering_header.txt"
            }
    

        ,
                "deseq2_vst": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Use vst transformation instead of rlog with DESeq2",
                "help_text": "Type: `boolean`. Use vst transformation instead of rlog with DESeq2"
            
            }
    

        ,
                "extra_deseq2_args": {
                "type":
                "string",
                "description": "Type: `string`, default: `--id_col 1 --sample_suffix \u0027\u0027 --outprefix deseq2 --count_col 3`. ",
                "help_text": "Type: `string`, default: `--id_col 1 --sample_suffix \u0027\u0027 --outprefix deseq2 --count_col 3`. "
            ,
                "default": "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
            }
    

        ,
                "extra_deseq2_args2": {
                "type":
                "string",
                "description": "Type: `string`, default: `star_salmon`. ",
                "help_text": "Type: `string`, default: `star_salmon`. "
            ,
                "default": "star_salmon"
            }
    

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

        ,
                "multiqc_title": {
                "type":
                "string",
                "description": "Type: `string`. ",
                "help_text": "Type: `string`. "
            
            }
    

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

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

        ,
                "num_trimmed_reads": {
                "type":
                "number",
                "description": "Type: `double`. ",
                "help_text": "Type: `double`. "
            
            }
    

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

        ,
                "percent_mapped": {
                "type":
                "number",
                "description": "Type: `double`. ",
                "help_text": "Type: `double`. "
            
            }
    

        ,
                "fastqc_zip_1": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

        ,
                "fastqc_zip_2": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

        ,
                "trim_zip_1": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

        ,
                "trim_zip_2": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

        ,
                "trim_log_1": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

        ,
                "trim_log_2": {
                "type":
                "string",
                "description": "Type: `file`. ",
                "help_text": "Type: `file`. "
            
            }
    

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

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

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

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

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

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

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

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

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

        ,
                "bamstat_output": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics",
                "help_text": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics"
            ,
                "default": "$id.$key.bamstat_output.txt"
            }
    

        ,
                "strandedness_output": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness",
                "help_text": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness"
            ,
                "default": "$id.$key.strandedness_output.txt"
            }
    

        ,
                "inner_dist_output_stats": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads",
                "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads"
            ,
                "default": "$id.$key.inner_dist_output_stats.stats"
            }
    

        ,
                "inner_dist_output_dist": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads"
            ,
                "default": "$id.$key.inner_dist_output_dist.txt"
            }
    

        ,
                "inner_dist_output_freq": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads"
            ,
                "default": "$id.$key.inner_dist_output_freq.txt"
            }
    

        ,
                "inner_dist_output_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads"
            ,
                "default": "$id.$key.inner_dist_output_plot.pdf"
            }
    

        ,
                "inner_dist_output_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads"
            ,
                "default": "$id.$key.inner_dist_output_plot_r.r"
            }
    

        ,
                "junction_annotation_output_log": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script"
            ,
                "default": "$id.$key.junction_annotation_output_log.log"
            }
    

        ,
                "junction_annotation_output_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot"
            ,
                "default": "$id.$key.junction_annotation_output_plot_r.r"
            }
    

        ,
                "junction_annotation_output_junction_bed": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)"
            ,
                "default": "$id.$key.junction_annotation_output_junction_bed.bed"
            }
    

        ,
                "junction_annotation_output_junction_interact": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization."
            ,
                "default": "$id.$key.junction_annotation_output_junction_interact.bed"
            }
    

        ,
                "junction_annotation_output_junction_sheet": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)"
            ,
                "default": "$id.$key.junction_annotation_output_junction_sheet.xls"
            }
    

        ,
                "junction_annotation_output_splice_events_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)"
            ,
                "default": "$id.$key.junction_annotation_output_splice_events_plot.pdf"
            }
    

        ,
                "junction_annotation_output_splice_junctions_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)",
                "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)"
            ,
                "default": "$id.$key.junction_annotation_output_splice_junctions_plot.pdf"
            }
    

        ,
                "junction_saturation_output_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot",
                "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot"
            ,
                "default": "$id.$key.junction_saturation_output_plot_r.r"
            }
    

        ,
                "junction_saturation_output_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf",
                "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf"
            ,
                "default": "$id.$key.junction_saturation_output_plot.pdf"
            }
    

        ,
                "read_distribution_output": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis",
                "help_text": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis."
            ,
                "default": "$id.$key.read_distribution_output.txt"
            }
    

        ,
                "read_duplication_output_duplication_rate_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot",
                "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot"
            ,
                "default": "$id.$key.read_duplication_output_duplication_rate_plot_r.r"
            }
    

        ,
                "read_duplication_output_duplication_rate_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)",
                "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)"
            ,
                "default": "$id.$key.read_duplication_output_duplication_rate_plot.pdf"
            }
    

        ,
                "read_duplication_output_duplication_rate_mapping": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication",
                "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication"
            ,
                "default": "$id.$key.read_duplication_output_duplication_rate_mapping.xls"
            }
    

        ,
                "read_duplication_output_duplication_rate_sequence": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication",
                "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication"
            ,
                "default": "$id.$key.read_duplication_output_duplication_rate_sequence.xls"
            }
    

        ,
                "tin_output_summary": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics",
                "help_text": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics"
            ,
                "default": "$id.$key.tin_output_summary.txt"
            }
    

        ,
                "tin_output_metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)",
                "help_text": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)"
            ,
                "default": "$id.$key.tin_output_metrics.xls"
            }
    

        ,
                "dupradar_output_dupmatrix": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts"
            ,
                "default": "$id.$key.dupradar_output_dupmatrix.txt"
            }
    

        ,
                "dupradar_output_dup_intercept_mqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar"
            ,
                "default": "$id.$key.dupradar_output_dup_intercept_mqc.txt"
            }
    

        ,
                "dupradar_output_duprate_exp_boxplot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot"
            ,
                "default": "$id.$key.dupradar_output_duprate_exp_boxplot.pdf"
            }
    

        ,
                "dupradar_output_duprate_exp_densplot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts"
            ,
                "default": "$id.$key.dupradar_output_duprate_exp_densplot.pdf"
            }
    

        ,
                "dupradar_output_duprate_exp_denscurve_mqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc"
            ,
                "default": "$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf"
            }
    

        ,
                "dupradar_output_expression_histogram": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram",
                "help_text": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram"
            ,
                "default": "$id.$key.dupradar_output_expression_histogram.pdf"
            }
    

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

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

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

        ,
                "deseq2_output": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. ",
                "help_text": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. "
            ,
                "default": "$id.$key.deseq2_output.deseq2_output"
            }
    

        ,
                "deseq2_output_pseudo": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.deseq2_output_pseudo.deseq2_output_pseudo`. ",
                "help_text": "Type: `file`, default: `$id.$key.deseq2_output_pseudo.deseq2_output_pseudo`. "
            ,
                "default": "$id.$key.deseq2_output_pseudo.deseq2_output_pseudo"
            }
    

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

}
},
    
    
    "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"
    }
]
}
