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Merge pull request #53 from tiagofilipe12/master
Adds a new example pipeline and edits existing example pipeline
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| 'use strict' | ||
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| // === WATERMILL === | ||
| const { | ||
| task, | ||
| join, | ||
| junction, | ||
| fork | ||
| } = require('../../..') | ||
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| // === MODULES === | ||
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| const fs = require('fs') | ||
| const path = require('path') | ||
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| const request = require('request') | ||
| const ncbi = require('bionode-ncbi') | ||
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| // === CONFIG === | ||
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| const THREADS = parseInt(process.env.WATERMILL_THREADS) || 2 | ||
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| const config = { | ||
| name: 'Streptococcus pneumoniae', | ||
| sraAccession: 'ERR045788', | ||
| referenceURL: 'http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/045/' + | ||
| 'GCF_000007045.1_ASM704v1/GCF_000007045.1_ASM704v1_genomic.fna.gz' | ||
| } | ||
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| // === TASKS === | ||
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| // first lets get the reference genome for our mapping | ||
| const getReference = task({ | ||
| params: { url: config.referenceURL }, | ||
| output: '*_genomic.fna.gz', | ||
| name: 'Download reference genome for ${config.name}' | ||
| }, ({ params, dir }) => { | ||
| const { url } = params | ||
| const outfile = url.split('/').pop() | ||
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| // essentially curl -O | ||
| return request(url).pipe(fs.createWriteStream(dir + '/' + outfile)) | ||
| }) | ||
|
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| //then get samples to work with | ||
| const getSamples = task({ | ||
| params: { | ||
| db: 'sra', | ||
| accession: config.sraAccession | ||
| }, | ||
| output: '**/*.sra', | ||
| dir: process.cwd(), // Set dir to resolve input/output from | ||
| name: 'Download SRA ${config.sraAccession}' | ||
| }, ({ params }) => `bionode-ncbi download ${params.db} ${params.accession}` ) | ||
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| // extract the samples from fastq.gz | ||
| const fastqDump = task({ | ||
| input: '**/*.sra', | ||
| output: [1, 2].map(n => `*_${n}.fastq.gz`), | ||
| name: 'fastq-dump **/*.sra' | ||
| }, ({ input }) => `fastq-dump --split-files --skip-technical --gzip ${input}` ) | ||
|
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| // then index using first bwa ... | ||
| const IndexReferenceBwa = task({ | ||
| input: '*_genomic.fna.gz', | ||
| output: ['amb', 'ann', 'bwt', 'pac', 'sa'].map(suffix => | ||
| `*_genomic.fna.gz.${suffix}`), | ||
| name: 'bwa index *_genomic.fna.gz' | ||
| }, ({ input }) => `bwa index ${input}`) | ||
|
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| // and bowtie2 | ||
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| const indexReferenceBowtie2 = task({ | ||
| input: '*_genomic.fna.gz', | ||
| output: ['1.bt2', '2.bt2', '3.bt2', '4.bt2', 'rev.1.bt2', | ||
| 'rev.2.bt2'].map(suffix => `bowtie_index.${suffix}`), | ||
| params: { output: 'bowtie_index'}, | ||
| name: 'bowtie2-build -q uncompressed.fa bowtie_index' | ||
| }, ({ params, input }) => `gunzip -c ${input} > uncompressed.fa | bowtie2-build -q uncompressed.fa ${params.output}` | ||
| ) | ||
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| // now use mappers with bwa | ||
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| const bwaMapper = task({ | ||
| input: { | ||
| reference: '*_genomic.fna.gz', | ||
| reads:[1, 2].map(n => `*_${n}.fastq.gz`), | ||
| indexFiles: ['amb', 'ann', 'bwt', 'pac', 'sa'].map(suffix => | ||
| `*_genomic.fna.gz.${suffix}`) //pass index files to bwa mem | ||
| }, | ||
| output: '*.sam', | ||
| params: {output: 'bwa_output.sam'}, | ||
| name: 'Mapping with bwa...' | ||
| }, ({ input, params }) => `bwa mem -t ${THREADS} ${input.reference} ${input.reads[0]} ${input.reads[1]} > ${params.output}` | ||
| ) | ||
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| // and with bowtie2 | ||
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| const bowtieMapper = task({ | ||
| input: { | ||
| reference: '*_genomic.fna.gz', | ||
| reads:[1, 2].map(n => `*_${n}.fastq.gz`), | ||
| indexFiles: ['1.bt2', '2.bt2', '3.bt2', '4.bt2', 'rev.1.bt2', | ||
| 'rev.2.bt2'].map(suffix => `bowtie_index.${suffix}`) //pass index files to | ||
| // bowtie2 | ||
| }, | ||
| output: '*.sam', | ||
| params: {output: 'bowtie2_output.sam'}, | ||
| name: 'Mapping with bowtie2...' | ||
| }, ({ input, params }) => `bowtie2 -p ${THREADS} -x bowtie_index -1 ${input.reads[0]} -2 ${input.reads[1]} -S ${params.output}` | ||
| ) | ||
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| // === PIPELINE === | ||
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| const pipeline = join( | ||
| junction( | ||
| getReference, | ||
| join(getSamples,fastqDump) | ||
| ), | ||
| fork( | ||
| join(IndexReferenceBwa, bwaMapper), | ||
| join(indexReferenceBowtie2, bowtieMapper) | ||
| ) | ||
| ) | ||
|
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| // actual run pipelines and return results | ||
| pipeline().then(results => console.log('PIPELINE RESULTS: ', results)) |
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