2021-01-29 18:31:33 +00:00
|
|
|
name: bowtie2_align
|
|
|
|
|
description: Align reads to a reference genome using bowtie2
|
|
|
|
|
keywords:
|
2022-02-15 11:15:27 +00:00
|
|
|
- align
|
|
|
|
|
- fasta
|
|
|
|
|
- genome
|
|
|
|
|
- reference
|
2021-01-29 18:31:33 +00:00
|
|
|
tools:
|
2022-02-15 11:15:27 +00:00
|
|
|
- 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"]
|
2021-01-29 18:31:33 +00:00
|
|
|
input:
|
2022-02-15 11:15:27 +00:00
|
|
|
- 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.
|
|
|
|
|
- index:
|
|
|
|
|
type: file
|
|
|
|
|
description: Bowtie2 genome index files
|
|
|
|
|
pattern: "*.ebwt"
|
2021-01-29 18:31:33 +00:00
|
|
|
output:
|
2022-02-15 11:15:27 +00:00
|
|
|
- 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"
|
2021-01-29 18:31:33 +00:00
|
|
|
authors:
|
2022-02-15 11:15:27 +00:00
|
|
|
- "@joseespinosa"
|
|
|
|
|
- "@drpatelh"
|
