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Merge pull request #15 from cancerit/feature/append_to_trimmed_reads
Feature/append to trimmed reads
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| // | ||
| // Utility functions used in nf-core DSL2 module files | ||
| // | ||
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| // | ||
| // Extract name of software tool from process name using $task.process | ||
| // | ||
| def getSoftwareName(task_process) { | ||
| return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() | ||
| } | ||
|
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| // | ||
| // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules | ||
| // | ||
| def initOptions(Map args) { | ||
| def Map options = [:] | ||
| options.args = args.args ?: '' | ||
| options.args2 = args.args2 ?: '' | ||
| options.args3 = args.args3 ?: '' | ||
| options.publish_by_meta = args.publish_by_meta ?: [] | ||
| options.publish_dir = args.publish_dir ?: '' | ||
| options.publish_files = args.publish_files | ||
| options.suffix = args.suffix ?: '' | ||
| return options | ||
| } | ||
|
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| // | ||
| // Tidy up and join elements of a list to return a path string | ||
| // | ||
| def getPathFromList(path_list) { | ||
| def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries | ||
| paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes | ||
| return paths.join('/') | ||
| } | ||
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| // | ||
| // Function to save/publish module results | ||
| // | ||
| def saveFiles(Map args) { | ||
| if (!args.filename.endsWith('.version.txt')) { | ||
| def ioptions = initOptions(args.options) | ||
| def path_list = [ ioptions.publish_dir ?: args.publish_dir ] | ||
| if (ioptions.publish_by_meta) { | ||
| def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta | ||
| for (key in key_list) { | ||
| if (args.meta && key instanceof String) { | ||
| def path = key | ||
| if (args.meta.containsKey(key)) { | ||
| path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] | ||
| } | ||
| path = path instanceof String ? path : '' | ||
| path_list.add(path) | ||
| } | ||
| } | ||
| } | ||
| if (ioptions.publish_files instanceof Map) { | ||
| for (ext in ioptions.publish_files) { | ||
| if (args.filename.endsWith(ext.key)) { | ||
| def ext_list = path_list.collect() | ||
| ext_list.add(ext.value) | ||
| return "${getPathFromList(ext_list)}/$args.filename" | ||
| } | ||
| } | ||
| } else if (ioptions.publish_files == null) { | ||
| return "${getPathFromList(path_list)}/$args.filename" | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| // Import generic module functions | ||
| include { initOptions; saveFiles; getSoftwareName } from './functions' | ||
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| params.options = [:] | ||
| options = initOptions(params.options) | ||
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| process APPEND_STRINGS_TO_FQ { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
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| publishDir "${params.outdir}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'modified_fastq', meta:meta, publish_by_meta:['id']) } | ||
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| input: | ||
| tuple val(meta), path(reads) | ||
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| output: | ||
| tuple val(meta), path("*.modified.fq.gz"), emit: reads | ||
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| script: | ||
| def software = getSoftwareName(task.process) | ||
| def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" | ||
| def input = reads | ||
| def append_start = params.append_start ? params.append_start : "" | ||
| def append_end = params.append_end ? params.append_end : "" | ||
| def append_quality_start = params.append_start ? params.append_quality*append_start.length() : "" | ||
| def append_quality_end = params.append_end ? params.append_quality*append_end.length() : "" | ||
| def output = "${prefix}.modified.fq.gz" | ||
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| $/ | ||
| zcat ${input} | \ | ||
| sed -e '2~4s/^\(.*\)$/${append_start}\1${append_end}/' -e '4~4s/^\(.*\)$/${append_quality_start}\1${append_quality_end}/' | \ | ||
| gzip > ${output} | ||
| /$ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| name: read modification | ||
| description: Manipulation of FASTQ files | ||
| keywords: | ||
| - FASTQ | ||
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| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:true ] | ||
| - reads: | ||
| type: file | ||
| description: | | ||
| List of input FASTQ files of size 1; i.e., single-end data. | ||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:true ] | ||
| - reads: | ||
| type: file | ||
| description: | | ||
| List of output FASTQ files of size 1; i.e., single-end data. | ||
| authors: | ||
| - "@vaofford" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| // | ||
| // Read modification | ||
| // | ||
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| params.options = [:] | ||
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| include { APPEND_STRINGS_TO_FQ } from '../../modules/local/read_modification/main' | ||
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| workflow READ_MODIFICATION { | ||
| take: | ||
| reads | ||
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| main: | ||
| ch_modified_reads = Channel.empty() | ||
| if (params.read_modification) { | ||
| // | ||
| // MODULE: Append string to reads | ||
| // | ||
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| APPEND_STRINGS_TO_FQ ( reads ) | ||
| ch_modified_reads = APPEND_STRINGS_TO_FQ.out.reads | ||
| } | ||
| emit: | ||
| reads = ch_modified_reads | ||
| } |
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