nf-core_modules/software/ivar/trim/meta.yml

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name: ivar_trim
description: Trim primer sequences rom a BAM file with iVar
keywords:
- amplicon sequencing
- trimming
- fasta
tools:
- ivar:
description: |
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
homepage: https://github.com/andersen-lab/ivar
documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
params:
- 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.
- enable_conda:
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.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
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description: Co-ordinate sorted BAM file
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pattern: "*.bam"
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- bai:
type: file
description: Index file for co-ordinate sorted BAM file
pattern: "*.bai"
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- bed:
type: file
description: BED file with primer labels and positions
pattern: "*.bed"
output:
- 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: iVar generated trimmed bam file (unsorted)
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pattern: "*.bam"
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- log:
type: file
description: Log file generated by iVar for use with MultiQC
pattern: "*.log"
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- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@andersgs"
- "@drpatelh"