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Merge pull request #31 from FelixKrueger/hisat2
Added HISAT2 module and test workflow
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commit
81b1d6081c
4 changed files with 131 additions and 0 deletions
58
tools/hisat2/main.nf
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58
tools/hisat2/main.nf
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nextflow.preview.dsl=2
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params.genome = ''
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process HISAT2 {
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// depending on the genome used one might want/need to adjust the memory settings.
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// For the E. coli test data this is probably not required
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// label 'bigMem'
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// label 'multiCore'
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input:
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tuple val(name), path(reads)
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val (outdir)
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val (hisat2_args)
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val (verbose)
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output:
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path "*bam", emit: bam
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path "*stats.txt", emit: stats
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publishDir "$outdir/hisat2",
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mode: "copy", overwrite: true
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script:
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if (verbose){
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println ("[MODULE] HISAT2 ARGS: " + hisat2_args)
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}
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cores = 4
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readString = ""
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hisat_options = hisat2_args
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// Options we add are
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hisat_options = hisat_options + " --no-unal --no-softclip "
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if (reads instanceof List) {
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readString = "-1 "+reads[0]+" -2 "+reads[1]
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hisat_options = hisat_options + " --no-mixed --no-discordant"
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}
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else {
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readString = "-U "+reads
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}
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index = params.genome["hisat2"]
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splices = ''
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if (params.genome.containsKey("hisat2_splices")){
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splices = " --known-splicesite-infile " + params.genome["hisat2_splices"]
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}
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else{
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println ("No key 'hisat2_splices' was supplied. Skipping...")
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}
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hisat_name = name + "_" + params.genome["name"]
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"""
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hisat2 -p ${cores} ${hisat_options} -x ${index} ${splices} ${readString} 2>${hisat_name}_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${hisat_name}_hisat2.bam
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"""
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}
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37
tools/hisat2/meta.yml
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37
tools/hisat2/meta.yml
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name: HISAT2
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description: Graph-based alignment of next generation sequencing reads to a population of genomes
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keywords:
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- Alignment
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- Short reads
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- graph FM Index (GFM)
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- RNA-seq
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tools:
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- fastqc:
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description: |
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HISAT2 is a fast and sensitive alignment program for mapping next-generation
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sequencing reads (whole-genome, transcriptome, and exome sequencing data)
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against the general human population (as well as against a single reference genome).
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Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
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graph FM index (GFM).
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homepage: http://daehwankimlab.github.io/hisat2/
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documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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- report:
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type: file
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description: mapping statistics report
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pattern: *hisat2_stats.txt
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- alignment:
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type: file
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description: alignment file in BAM format
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pattern: *hisat2.bam
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authors:
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- @FelixKrueger
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34
tools/hisat2/test/main.nf
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34
tools/hisat2/test/main.nf
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#!/usr/bin/env nextflow
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nextflow.preview.dsl=2
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params.outdir = "."
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params.genome = ""
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params.hisat2_args = ''
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// HISAT2 arguments should be supplied in the following format to work:
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// --hisat2_args="--score-min L,0,-0.8"
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params.verbose = false
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if (params.verbose){
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println ("[WORKFLOW] HISAT2 ARGS ARE: " + params.hisat2_args)
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}
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// for other genomes this needs to be handled somehow to return all possible genomes
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genomeValues = ["name" : params.genome]
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genomeValues["hisat2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/hisat2/E_coli/${params.genome}";
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include '../main.nf' params(genome: genomeValues)
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ch_read_files = Channel
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.fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
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// .view() // to check whether the input channel works
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workflow {
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main:
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HISAT2(ch_read_files, params.outdir, params.hisat2_args, params.verbose)
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}
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2
tools/hisat2/test/nextflow.config
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2
tools/hisat2/test/nextflow.config
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// docker.enabled = true
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params.outdir = './results'
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