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schema.nf
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schema.nf
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#! /usr/bin/env nextflow
/*
*
* SCHEMA DEFINITION FOR PARAMS VALIDATION
*
*/
def Map schema = [:] // don't change this line
// --------------------------------------------------------------------------------------------------------------
// generic options:
schema.title1 = [title: 'GENERIC OPTIONS']
schema.min_nf_version = [value: '21.10.6', type: 'string', mandatory: true, allowed: '']
schema.publishmode = [value: 'copy', type: 'string', mandatory: true, allowed:['symlink', 'rellink', 'link', 'copy', 'copyNoFollow', 'move']]
schema.outdir = [value: "$launchDir/rnaseq_preprocess_results/", type: 'string', mandatory: true]
schema.pipe_dir = [value: "${schema.outdir['value']}/pipeline_info/", type: 'string']
// indexing:
schema.title2 = [title: 'INDEXING OPTIONS']
schema.idx = [value: '', type: 'string']
schema.tx2gene = [value: '', type: 'string']
schema.txtome = [value: '', type: 'string', pattern: /.*\.gz$/]
schema.genome = [value: '', type: 'string', pattern: /.*\.gz$/]
schema.gtf = [value: '', type: 'string', pattern: /.*\.gz$/]
schema.transcript_id = [value: 'transcript_id', type: 'string']
schema.transcript_name = [value: 'transcript_name', type: 'string']
schema.gene_id = [value: 'gene_id', type: 'string']
schema.gene_name = [value: 'gene_name', type: 'string']
schema.gene_type = [value: 'gene_type', type: 'string']
schema.idx_name = [value: "idx", type: 'string']
schema.idx_dir = [value: "${schema.outdir['value']}/salmon_idx/", type: 'string']
schema.idx_additional = [value: '--gencode', type: 'string']
schema.only_idx = [value: false, type: 'logical']
// combining technical replicates into a single fastq and trimming
schema.title3 = [title: 'MERGE/FASTQ OPTIONS']
schema.merge_dir = [value: "${schema.outdir['value']}/fastq_merged/", type: 'string']
schema.merge_keep = [value: false, type: 'logical']
schema.trim_reads = [value: false, type: 'logical']
schema.trim_dir = [value: "${schema.outdir['value']}/fastq_trimmed/", type: 'string']
schema.trim_length = [value: 75, type: 'numeric']
schema.trim_keep = [value: false, type: 'logical']
// fastqc/multiqc
schema.title4 = [title: 'FASTQC/MULTIQC OPTIONS']
schema.skip_fastqc = [value: false, type: 'logical']
schema.skip_multiqc = [value: false, type: 'logical']
schema.fastqc_dir = [value: "${schema.outdir['value']}/fastqc/", type: 'string']
schema.multiqc_dir = [value: "${schema.outdir['value']}/multiqc/", type: 'string']
schema.only_fastqc = [value: false, type: 'logical']
// samplesheet and quantification
schema.title5 = [title: 'QUANTIFICATION/TXIMPORT OPTIONS']
schema.samplesheet = [value: '', type: 'string', pattern: /.*\.csv$/]
schema.quant_dir = [value: "${schema.outdir['value']}/salmon_quant/", type: 'string']
schema.quant_additional = [value: '--gcBias --seqBias --posBias', type: 'string']
schema.tximport_dir = [value: "${schema.outdir['value']}/tximport/", type: 'string']
schema.skip_tximport = [value: false, type: 'logical']
// related to the container/environment for the R/Bioconductor part of this workflow
schema.title6 = [title: 'CONTAINER/CONDA OPTIONS']
schema.container = [value: 'atpoint/rnaseq_preprocess:v1.7.2', type: 'string', mandatory: true]
schema.environment = [value: "$baseDir/environment.yml", type:'string', mandatory: true ]
// --------------------------------------------------------------------------------------------------------------
return schema // don't change this line