435 lines
15 KiB
JSON
435 lines
15 KiB
JSON
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{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "post_processing",
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"description": "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline.\n",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"id": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `foo`. ID of the sample",
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"help_text": "Type: `string`, required, example: `foo`. ID of the sample."
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}
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,
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"strandedness": {
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"type":
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"string",
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"description": "Type: `string`, default: `auto`. Sample strand-specificity",
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"help_text": "Type: `string`, default: `auto`. Sample strand-specificity. Must be one of unstranded, forward, reverse or auto"
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,
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"default": "auto"
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}
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,
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"paired": {
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"type":
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"boolean",
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"description": "Type: `boolean`. Paired fastq files or not?",
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"help_text": "Type: `boolean`. Paired fastq files or not?"
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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`, required. Path to FASTA genome file",
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"help_text": "Type: `file`, required. Path to FASTA genome file."
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}
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,
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"fai": {
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"type":
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"string",
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"description": "Type: `file`, required. Path to FASTA index",
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"help_text": "Type: `file`, required. Path to FASTA index"
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}
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,
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"gtf": {
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"type":
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"string",
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"description": "Type: `file`. GTF file",
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"help_text": "Type: `file`. GTF file"
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}
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,
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"genome_bam": {
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"type":
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"string",
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"description": "Type: `file`. Genome BAM file",
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"help_text": "Type: `file`. Genome BAM file"
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}
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,
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"chrom_sizes": {
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"type":
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"string",
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"description": "Type: `file`. File containing chromosome lengths",
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"help_text": "Type: `file`. File containing chromosome lengths"
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}
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,
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"star_multiqc": {
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"type":
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"string",
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"description": "Type: `file`. STAR align log file",
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"help_text": "Type: `file`. STAR align log file."
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}
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,
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"extra_picard_args": {
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"type":
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"string",
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"description": "Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline",
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"help_text": "Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline."
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,
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"default": ""
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}
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,
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"extra_stringtie_args": {
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"type":
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"string",
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"description": "Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline",
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"help_text": "Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline."
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,
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"default": ""
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}
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,
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"stringtie_ignore_gtf": {
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"type":
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"boolean",
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"description": "Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i",
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"help_text": "Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don\u0027t restrict to those in GTF file."
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}
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,
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"extra_bedtools_args": {
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"type":
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"string",
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"description": "Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline",
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"help_text": "Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline."
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,
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"default": ""
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}
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,
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"bam_csi_index": {
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"type":
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"boolean",
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"description": "Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index",
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"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."
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,
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"default": "False"
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}
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,
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"min_mapped_reads": {
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"type":
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"integer",
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"description": "Type: `integer`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing",
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"help_text": "Type: `integer`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing."
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}
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,
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"with_umi": {
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"type":
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"boolean",
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"description": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication",
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"help_text": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication."
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"default": "False"
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}
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,
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"skip_qc": {
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"type":
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"boolean",
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"description": "Type: `boolean`. ",
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"help_text": "Type: `boolean`. "
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}
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,
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"skip_markduplicates": {
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"type":
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"boolean",
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"description": "Type: `boolean`. ",
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"help_text": "Type: `boolean`. "
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}
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,
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"skip_stringtie": {
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"type":
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"boolean",
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"description": "Type: `boolean`. ",
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"help_text": "Type: `boolean`. "
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}
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,
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"skip_bigwig": {
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"type":
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"boolean",
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"description": "Type: `boolean`. ",
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"help_text": "Type: `boolean`. "
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}
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}
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},
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"output" : {
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"title": "Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"processed_genome_bam": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. ",
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"help_text": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. "
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,
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"default": "$id.$key.processed_genome_bam.bam"
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}
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,
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"genome_bam_index": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.genome_bam_index.bam`. ",
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"help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bam`. "
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,
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"default": "$id.$key.genome_bam_index.bam"
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}
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,
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"genome_bam_stats": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ",
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"help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. "
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"default": "$id.$key.genome_bam_stats.stats"
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}
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,
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"genome_bam_flagstat": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ",
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"help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. "
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"default": "$id.$key.genome_bam_flagstat.flagstat"
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}
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,
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"genome_bam_idxstats": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ",
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"help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. "
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,
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"default": "$id.$key.genome_bam_idxstats.idxstats"
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}
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,
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"markduplicates_metrics": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. ",
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"help_text": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. "
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,
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"default": "$id.$key.markduplicates_metrics.txt"
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}
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,
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"stringtie_transcript_gtf": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. ",
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"help_text": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. "
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,
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"default": "$id.$key.stringtie_transcript_gtf.gtf"
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}
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,
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"stringtie_coverage_gtf": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. ",
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"help_text": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. "
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,
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"default": "$id.$key.stringtie_coverage_gtf.gtf"
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}
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,
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"stringtie_abundance": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. ",
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"help_text": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. "
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,
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"default": "$id.$key.stringtie_abundance.txt"
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}
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,
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"stringtie_ballgown": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. ",
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"help_text": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. "
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,
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"default": "$id.$key.stringtie_ballgown.ballgown"
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}
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,
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"bedgraph_forward": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ",
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"help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. "
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,
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"default": "$id.$key.bedgraph_forward.bedgraph"
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}
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,
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"bedgraph_reverse": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ",
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"help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. "
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,
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"default": "$id.$key.bedgraph_reverse.bedgraph"
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}
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,
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"bigwig_forward": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. ",
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"help_text": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. "
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,
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"default": "$id.$key.bigwig_forward.bigwig"
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}
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,
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"bigwig_reverse": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. ",
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"help_text": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. "
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,
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"default": "$id.$key.bigwig_reverse.bigwig"
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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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|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
,
|
||
|
|
"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"
|
||
|
|
}
|
||
|
|
]
|
||
|
|
}
|