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Merge pull request #266 from FriederikeHanssen/dsl2_variantcalling
Variantcalling
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| /* | ||
| * ------------------------------------------------- | ||
| * Nextflow config file for running tests | ||
| * ------------------------------------------------- | ||
| * Defines bundled input files and everything required | ||
| * to run a fast and simple test. Use as follows: | ||
| * nextflow run nf-core/sarek -profile test_tool | ||
| */ | ||
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| includeConfig 'test.config' | ||
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| params { | ||
| // Input data | ||
| tools = 'haplotypecaller,strelka' | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| /* | ||
| * ----------------------------------------------------- | ||
| * Utility functions used in nf-core DSL2 module files | ||
| * ----------------------------------------------------- | ||
| */ | ||
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| /* | ||
| * Extract name of software tool from process name using $task.process | ||
| */ | ||
| def getSoftwareName(task_process) { | ||
| return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() | ||
| } | ||
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| /* | ||
| * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules | ||
| */ | ||
| def initOptions(Map args) { | ||
| def Map options = [:] | ||
| options.args = args.args ?: '' | ||
| options.args2 = args.args2 ?: '' | ||
| options.publish_by_id = args.publish_by_id ?: false | ||
| options.publish_dir = args.publish_dir ?: '' | ||
| options.publish_files = args.publish_files ?: null | ||
| options.suffix = args.suffix ?: '' | ||
| return options | ||
| } | ||
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| /* | ||
| * Tidy up and join elements of a list to return a path string | ||
| */ | ||
| def getPathFromList(path_list) { | ||
| def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries | ||
| paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes | ||
| return paths.join('/') | ||
| } | ||
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| /* | ||
| * Function to save/publish module results | ||
| */ | ||
| def saveFiles(Map args) { | ||
| if (!args.filename.endsWith('.version.txt')) { | ||
| def ioptions = initOptions(args.options) | ||
| def path_list = [ ioptions.publish_dir ?: args.publish_dir ] | ||
| if (ioptions.publish_by_id) { | ||
| path_list.add(args.publish_id) | ||
| } | ||
| if (ioptions.publish_files instanceof Map) { | ||
| for (ext in ioptions.publish_files) { | ||
| if (args.filename.endsWith(ext.key)) { | ||
| def ext_list = path_list.collect() | ||
| ext_list.add(ext.value) | ||
| return "${getPathFromList(ext_list)}/$args.filename" | ||
| } | ||
| } | ||
| } else { | ||
| return "${getPathFromList(path_list)}/$args.filename" | ||
| } | ||
| } | ||
| } |
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| process GATK_GENOTYPEVCF { | ||
| tag "${meta.id}-${interval.baseName}" | ||
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| input: | ||
| tuple val(meta), path(interval), path(gvcf) | ||
| path dbsnp | ||
| path dbsnpIndex | ||
| path dict | ||
| path fasta | ||
| path fai | ||
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| output: | ||
| tuple val("HaplotypeCaller"), val(meta), path("${interval.baseName}_${meta.id}.vcf") | ||
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| script: | ||
| // Using -L is important for speed and we have to index the interval files also | ||
| intervalsOptions = params.no_intervals ? "" : "-L ${interval}" | ||
| dbsnpOptions = params.dbsnp ? "--D ${dbsnp}" : "" | ||
| """ | ||
| gatk --java-options -Xmx${task.memory.toGiga()}g \ | ||
| IndexFeatureFile \ | ||
| -I ${gvcf} | ||
| gatk --java-options -Xmx${task.memory.toGiga()}g \ | ||
| GenotypeGVCFs \ | ||
| -R ${fasta} \ | ||
| ${intervalsOptions} \ | ||
| ${dbsnpOptions} \ | ||
| -V ${gvcf} \ | ||
| -O ${interval.baseName}_${meta.id}.vcf | ||
| """ | ||
| } |
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