2021-02-12 19:25:40 +00:00
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name: ivar_consensus
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description: Generate a consensus sequence from a BAM file using iVar
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keywords:
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- amplicon sequencing
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- consensus
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- fasta
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tools:
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- ivar:
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description: |
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2021-02-12 22:46:13 +00:00
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iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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2021-02-12 19:25:40 +00:00
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homepage: https://github.com/andersen-lab/ivar
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documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
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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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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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- bam:
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type: file
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description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file
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pattern: "*.bam"
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- ref:
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type: file
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description: The reference sequence used for mapping and generating the BAM file
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pattern: "*.fa"
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output:
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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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- fasta:
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type: file
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description: iVar generated consensus sequence
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pattern: "*.fa"
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- qual:
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type: file
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description: iVar generated quality file
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pattern: "*.qual.txt"
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2021-02-12 22:46:13 +00:00
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- mpileup:
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2021-02-12 19:25:40 +00:00
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type: file
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description: mpileup output from samtools mpileup [OPTIONAL]
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pattern: "*.mpileup"
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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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authors:
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- "@andersgs"
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- "@drpatelh"
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