nf-core_modules/software/salmon/quant/meta.yml
Kevin Menden afaef3c30d
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 12:40:15 +01:00

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YAML

name: salmon_quant
description: gene/transcript quantification with Salmon
keywords:
- index
- fasta
- genome
- reference
tools:
- salmon:
description: |
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
homepage: https://salmon.readthedocs.io/en/latest/salmon.html
manual: https://salmon.readthedocs.io/en/latest/salmon.html
doi: 10.1038/nmeth.4197
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: directory
description: Folder containing the star index files
- gtf:
type: file
description: GTF of the reference transcriptome
- transcriptome_fasta:
type: file
description: Fasta file of the reference transcriptome
- alignment_mode:
type: boolean
description: whether to run salmon in alignment mode
output:
- sample_output:
type: directory
description: Folder containing the quantification results for a specific sample
pattern: "${prefix}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"
- "@drpatelh"