2022-04-03 05:58:40 +00:00
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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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2022-09-08 06:08:36 +00:00
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- map
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2022-04-03 05:58:40 +00:00
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- fasta
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2022-09-08 06:08:36 +00:00
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- fastq
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2022-04-03 05:58:40 +00:00
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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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licence: ["GPL-3.0-or-later"]
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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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2022-12-23 16:23:05 +00:00
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- meta2:
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type: map
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description: |
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Groovy Map containing reference information
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e.g. [ id:'test', single_end:false ]
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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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2022-09-08 06:08:36 +00:00
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- save_unaligned:
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type: boolean
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description: |
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Save reads that do not map to the reference (true) or discard them (false)
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(default: false)
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- sort_bam:
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type: boolean
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description: use samtools sort (true) or samtools view (false)
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pattern: "true or false"
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2022-04-03 05:58:40 +00:00
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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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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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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