Merge pull request #18 from annacprice/shovill

initial commit of shovill
This commit is contained in:
Phil Ewels 2020-07-11 13:00:43 +02:00 committed by GitHub
commit 21711813c1
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
4 changed files with 72 additions and 0 deletions

20
tools/shovill/main.nf Normal file
View file

@ -0,0 +1,20 @@
process shovill {
tag { shovill }
publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'
container "quay.io/biocontainers/shovill:1.0.9--0"
input:
tuple(sample_id, path(forward), path(reverse))
output:
path("${sample_id}.fasta")
script:
"""
shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
mv shovill_out/contigs.fa ${sample_id}.fasta
"""
}

30
tools/shovill/meta.yml Normal file
View file

@ -0,0 +1,30 @@
name: Shovill
description: Create a bacterial assembly from paired fastq using shovill
keywords:
- Genome Assembly
- Bacterial Isolates
tools:
- fastqc:
description: |
Shovill assembles bacterial isolate genomes from Illumina
paired-end reads. Shovill uses the SPAdes genome assembler,
providing pre and post-processing to the SPAdes assembly.
It also supports SKESA, Velvet and Megahit.
homepage: https://github.com/tseemann/shovill
documentation: https://github.com/tseemann/shovill/blob/master/README.md
input:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: pair of fastq files
output:
-
- assembly:
type: file
description: fasta file
pattern: ${sample_id}.fasta
authors:
- @annacprice

View file

@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
// import shovill
include {shovill} from '../main.nf' params(params)
// define input channel
readsPath = '../../../test-datasets/tools/shovill/input/SRR3609257_{1,2}.fastq.gz'
Channel
.fromFilePairs( "${readsPath}", flat: true )
.set{ ch_reads }
// main workflow
workflow {
shovill(ch_reads)
}

View file

@ -0,0 +1,5 @@
// docker
docker.enabled = true
// output directory
params.outdir = './results'