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74 lines
2.4 KiB
YAML
74 lines
2.4 KiB
YAML
name: bowtie2_align
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description: Align reads to a reference genome using bowtie2
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keywords:
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- align
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- fasta
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- genome
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- reference
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tools:
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- bowtie2:
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description: |
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Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences.
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homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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doi: 10.1038/nmeth.1923
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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- save_unaligned:
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type: boolean
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description: Save unaligned reads
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: file
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description: Bowtie2 genome index files
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pattern: "*.ebwt"
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output:
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- fastq:
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type: file
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description: Unaligned FastQ files
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pattern: "*.fastq.gz"
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- log:
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type: file
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description: Aligment log
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pattern: "*.log"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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