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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| /* | ||
| * This file holds several functions used to perform standard checks for the nf-core/viralrecon pipeline. | ||
| */ | ||
|
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| class Workflow { | ||
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| // Citation string | ||
| private static String citation(workflow) { | ||
| return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + | ||
| "* The pipeline\n" + | ||
| " https://doi.org/10.5281/zenodo.1400710\n\n" + | ||
| "* The nf-core framework\n" + | ||
| " https://doi.org/10.1038/s41587-020-0439-x\n\n" + | ||
| "* Software dependencies\n" + | ||
| " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" | ||
| } | ||
|
|
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| static void validate_params(params, log, valid_params) { | ||
| genome_exists(params, log) | ||
|
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| // Generic parameter validation | ||
| if (!params.fasta) { | ||
| log.error "Genome fasta file not specified!" | ||
| System.exit(0) | ||
| } | ||
|
|
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| if (!params.skip_kraken2 && !params.kraken2_db) { | ||
| if (!params.kraken2_db_name) { | ||
| log.error "Please specify a valid name to build Kraken2 database for host e.g. 'human'!" | ||
| System.exit(0) | ||
| } | ||
| } | ||
|
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| if (!valid_params['protocols'].contains(params.protocol)) { | ||
| log.error "Invalid protocol option: ${params.protocol}. Valid options: ${valid_params['protocols'].join(', ')}" | ||
| System.exit(0) | ||
| } | ||
|
|
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| // Variant calling parameter validation | ||
| def callers = params.callers ? params.callers.split(',').collect{ it.trim().toLowerCase() } : [] | ||
| if ((valid_params['callers'] + callers).unique().size() != valid_params['callers'].size()) { | ||
| log.error "Invalid variant calller option: ${params.callers}. Valid options: ${valid_params['callers'].join(', ')}" | ||
| System.exit(0) | ||
| } | ||
|
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| if (params.protocol == 'amplicon' && !params.skip_variants && !params.primer_bed) { | ||
| log.error "To perform variant calling in 'amplicon' mode please provide a valid primer BED file!" | ||
| System.exit(0) | ||
| } | ||
|
|
||
| // Assembly parameter validation | ||
| def assemblers = params.assemblers ? params.assemblers.split(',').collect{ it.trim().toLowerCase() } : [] | ||
| if ((valid_params['assemblers'] + assemblers).unique().size() != valid_params['assemblers'].size()) { | ||
| log.error "Invalid assembler option: ${params.assemblers}. Valid options: ${valid_params['assemblers'].join(', ')}" | ||
| System.exit(0) | ||
| } | ||
|
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| if (!valid_params['spades_modes'].contains(params.spades_mode)) { | ||
| log.error "Invalid spades mode option: ${params.spades_mode}. Valid options: ${valid_params['spades_modes'].join(', ')}" | ||
| System.exit(0) | ||
| } | ||
| } | ||
|
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| // Print a warning after SRA download has completed | ||
| static void sra_download(log) { | ||
| log.warn "=============================================================================\n" + | ||
| " THIS IS AN EXPERIMENTAL FEATURE!\n\n" + | ||
| " Please double-check the samplesheet that has been auto-created using the\n" + | ||
| " public database ids provided via the '--public_data_ids' parameter.\n\n" + | ||
| " All of the sample metadata obtained from the ENA has been appended\n" + | ||
| " as additional columns to help you manually curate the samplesheet before\n" + | ||
| " you run the main branch of the pipeline.\n" + | ||
| "===================================================================================" | ||
| } | ||
|
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| // Exit pipeline if incorrect --genome key provided | ||
| static void genome_exists(params, log) { | ||
| if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { | ||
| log.error "=============================================================================\n" + | ||
| " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + | ||
| " Currently, the available genome keys are:\n" + | ||
| " ${params.genomes.keySet().join(", ")}\n" + | ||
| "===================================================================================" | ||
| System.exit(0) | ||
| } | ||
| } | ||
|
|
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| // Get attribute from genome config file e.g. fasta | ||
| static String get_genome_attribute(params, attribute) { | ||
| def val = '' | ||
| if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { | ||
| if (params.genomes[ params.genome ].containsKey(attribute)) { | ||
| val = params.genomes[ params.genome ][ attribute ] | ||
| } | ||
| } | ||
| return val | ||
| } | ||
|
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| // Print warning if genome fasta has more than one sequence | ||
| static void is_multifasta(fasta, log) { | ||
| def count = 0 | ||
| def line = null | ||
| fasta.withReader { reader -> | ||
| while (line = reader.readLine()) { | ||
| if (line.contains('>')) { | ||
| count++ | ||
| if (count > 1) { | ||
| log.warn "=============================================================================\n" + | ||
| " This pipeline does not officially support multi-fasta genome files!\n\n" + | ||
| " The parameters and processes are tailored for viral genome analysis.\n" + | ||
| " Please amend the '--fasta' parameter.\n" + | ||
| "===================================================================================" | ||
| break | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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| // Function that parses and returns the number of mapped reasds from flagstat files | ||
| static ArrayList get_flagstat_mapped_reads(workflow, params, log, flagstat) { | ||
| def mapped_reads = 0 | ||
| flagstat.eachLine { line -> | ||
| if (line.contains(' mapped (')) { | ||
| mapped_reads = line.tokenize().first().toInteger() | ||
| } | ||
| } | ||
|
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| def pass = false | ||
| def logname = flagstat.getBaseName() - 'flagstat' | ||
| Map colors = Headers.log_colours(params.monochrome_logs) | ||
| if (mapped_reads <= params.min_mapped_reads.toInteger()) { | ||
| log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} [FAIL] Mapped read threshold >= ${params.min_mapped_reads}. IGNORING FOR FURTHER DOWNSTREAM ANALYSIS: ${mapped_reads} - $logname${colors.reset}." | ||
| } else { | ||
| pass = true | ||
| //log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} [PASS] Mapped read threshold >=${params.min_mapped_reads}: ${mapped_reads} - $logname${colors.reset}." | ||
| } | ||
| return [ mapped_reads, pass ] | ||
| } | ||
|
|
||
| } |
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