Merge pull request #1622 from matthdsm/update/snapaligner

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Matthias De Smet 2022-05-06 19:34:09 +02:00 committed by GitHub
commit b6dd8d2854
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13 changed files with 58 additions and 159 deletions

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@ -1,4 +1,4 @@
process SNAPALIGNER_PAIRED { process SNAPALIGNER_ALIGN {
tag '$meta.id' tag '$meta.id'
label 'process_high' label 'process_high'
@ -21,15 +21,16 @@ process SNAPALIGNER_PAIRED {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def subcmd = meta.single_end ? "single" : "paired"
""" """
mkdir -p index mkdir -p index
mv $index index/ mv $index index/
snap-aligner paired \\ snap-aligner ${subcmd} \\
index \\ index \\
${reads.join(" ")} \\ ${reads.join(" ")} \\
-o -bam ${prefix}.bam \\ -o ${prefix}.bam \\
-t ${task.cpus} \\ -t ${task.cpus} \\
$args $args

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@ -1,5 +1,5 @@
name: "snapaligner_paired" name: "snapaligner_align"
description: Performs paired end fastq alignment to a fasta reference using SNAP description: Performs fastq alignment to a fasta reference using SNAP
keywords: keywords:
- alignment - alignment
- map - map
@ -22,7 +22,7 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- reads: - reads:
type: file type: file
description: List of input fastq files of size 2 for fastq or 1 for bam description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
- index: - index:
type: file type: file

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@ -1,41 +0,0 @@
process SNAPALIGNER_SINGLE {
tag '$meta.id'
label 'process_high'
conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p index
mv $index index/
snap-aligner single \\
index \\
${reads.join(" ")} \\
-o -bam ${prefix}.bam \\
-t ${task.cpus} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
END_VERSIONS
"""
}

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@ -1,48 +0,0 @@
name: "snapaligner_single"
description: Performs single end fastq alignment to a fasta reference using SNAP
keywords:
- alignment
- map
- fastq
- bam
- sam
tools:
- "snapaligner":
description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
homepage: "http://snap.cs.berkeley.edu"
documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
tool_dev_url: "https://github.com/amplab/snap"
doi: "10.1101/2021.11.23.469039"
licence: "['Apache v2']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: List of single end input files
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
- index:
type: file
description: List of SNAP genome index files
pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Aligned BAM file
pattern: "*.{bam}"
authors:
- "@matthdsm"

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@ -1767,13 +1767,9 @@ snapaligner/index:
- modules/snapaligner/index/** - modules/snapaligner/index/**
- tests/modules/snapaligner/index/** - tests/modules/snapaligner/index/**
snapaligner/paired: snapaligner/align:
- modules/snapaligner/paired/** - modules/snapaligner/align/**
- tests/modules/snapaligner/paired/** - tests/modules/snapaligner/align/**
snapaligner/single:
- modules/snapaligner/single/**
- tests/modules/snapaligner/single/**
snpdists: snpdists:
- modules/snpdists/** - modules/snpdists/**

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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
workflow test_snapaligner_single {
input = [
[ id:'test', single_end:true ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
}
workflow test_snapaligner_paired {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
}

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@ -0,0 +1,19 @@
- name: snapaligner align test_snapaligner_single
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_single -c tests/config/nextflow.config
tags:
- snapaligner/align
- snapaligner
files:
- path: output/snapaligner/test.bam
md5sum: 5d95594e4ef1ee23ce56e6a7cb64f0f2
- path: output/snapaligner/versions.yml
- name: snapaligner align test_snapaligner_paired
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_paired -c tests/config/nextflow.config
tags:
- snapaligner/align
- snapaligner
files:
- path: output/snapaligner/test.bam
md5sum: a1405da5876f15dbe8a81516b94c2a15
- path: output/snapaligner/versions.yml

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@ -1,17 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
include { SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/paired/main.nf'
workflow test_snapaligner_paired {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
}

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@ -1,9 +0,0 @@
- name: snapaligner paired test_snapaligner_paired
command: nextflow run tests/modules/snapaligner/paired -entry test_snapaligner_paired -c tests/config/nextflow.config
tags:
- snapaligner
- snapaligner/paired
files:
- path: output/snapaligner/test.bam
md5sum: 2ac92e9539fa246dd6db52b5de56fca5
- path: output/snapaligner/versions.yml

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@ -1,17 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
include { SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/single/main.nf'
workflow test_snapaligner_single {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
}

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@ -1,5 +0,0 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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@ -1,9 +0,0 @@
- name: snapaligner single test_snapaligner_single
command: nextflow run tests/modules/snapaligner/single -entry test_snapaligner_single -c tests/config/nextflow.config
tags:
- snapaligner/single
- snapaligner
files:
- path: output/snapaligner/test.bam
md5sum: 696f7ea8e1aa5f9d7dafb9d0134fe25d
- path: output/snapaligner/versions.yml