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56 lines
1.7 KiB
YAML
56 lines
1.7 KiB
YAML
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name: cat_fastq
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description: Concatenates fastq files
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keywords:
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- fastq
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- concatenate
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tools:
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- cat:
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description: |
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The cat utility reads files sequentially, writing them to the standard output.
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documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.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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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: list
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description: |
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List of input FastQ files to be concatenated.
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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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- reads:
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type: file
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description: Merged fastq file
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pattern: "*.{merged.fastq.gz}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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