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Fixing meta ymls

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JoseEspinosa 2021-02-01 09:28:51 +01:00
parent b6ef06c6cd
commit eb12f4610d
2 changed files with 77 additions and 67 deletions
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71
software/bcftools/bgzip/meta.yml
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@ -6,50 +6,55 @@ keywords:
- VCF
tools:
- bgzip:
description: |
Bgzip compresses files in a similar manner to, and compatible with, gzip.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bgzip.html
doi: 10.1093/bioinformatics/btp352
description: |
Bgzip compresses files in a similar manner to, and compatible with, gzip.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bgzip.html
doi: 10.1093/bioinformatics/btp352
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
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
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.
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 ]
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF text file
type: file
description: VCF text file
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: Output compressed VCF file
pattern: "*.{vcf}"
type: file
description: Output compressed VCF file
pattern: "*.{vcf}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

73
software/bcftools/consensus/meta.yml
View file

@ -6,59 +6,64 @@ keywords:
- VCF
tools:
- consensus:
description: |
Create consensus sequence by applying VCF variants to a reference fasta file.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
description: |
Create consensus sequence by applying VCF variants to a reference fasta file.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
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
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.
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 ]
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF file
pattern: "*.{vcf}"
type: file
description: VCF file
pattern: "*.{vcf}"
- tbi:
type: file
description: tabix index file
pattern: "*.{tbi}"
type: file
description: tabix index file
pattern: "*.{tbi}"
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA reference consensus file
pattern: "*.{fasta,fa}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"