nf-core_modules/software/TOOL/SUBTOOL/meta.yml

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## 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
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
- bam
- sam
- cram
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tools:
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## TODO nf-core: Change the name of the tool below
- samtools:
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## TODO nf-core: Add a description and other details for the software below
description: |
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SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
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
params:
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- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
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:
type: map
description: |
Groovy Map containing sample information
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
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:
type: map
description: |
Groovy Map containing sample information
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
pattern: "*.{bam,cram,sam}"
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- version:
type: file
description: File containing software version
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"