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meta.yml
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meta.yml
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name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
- align
- map
- fasta
- fastq
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- meta2:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'test', single_end:false ]
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
- save_unaligned:
type: boolean
description: |
Save reads that do not map to the reference (true) or discard them (false)
(default: false)
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- log:
type: file
description: Aligment log
pattern: "*.log"
authors:
- "@joseespinosa"
- "@drpatelh"