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72 lines
2.7 KiB
YAML
72 lines
2.7 KiB
YAML
## TODO nf-core: Please delete all of these TODO statements once the file has been curated
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## TODO nf-core: Change the name of "tool_subtool" below
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name: tool_subtool
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## TODO nf-core: Add a description and keywords
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description: Sort SAM/BAM/CRAM file
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keywords:
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- sort
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- bam
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- sam
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- cram
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tools:
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## TODO nf-core: Change the name of the tool below
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- samtools:
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## TODO nf-core: Add a description and other details for the software below
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: http://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below
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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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## TODO nf-core: Add a description of all of the variables used as 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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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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## TODO nf-core: Add a description of all of the variables used as output
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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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- bam:
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type: file
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description: Sorted BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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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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## TODO nf-core: Add your GitHub username below
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authors:
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- "@your_github_username"
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