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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 - VCF
tools: tools:
- bgzip: - bgzip:
description: | description: |
Bgzip compresses files in a similar manner to, and compatible with, gzip. Bgzip compresses files in a similar manner to, and compatible with, gzip.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bgzip.html documentation: http://www.htslib.org/doc/bgzip.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
params: params:
- outdir: - outdir:
type: string type: string
description: | description: |
The pipeline's output directory. By default, the module will The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>` output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode: - publish_dir_mode:
type: string type: string
description: | description: |
Value for the Nextflow `publishDir` mode parameter. Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move. Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda: - enable_conda:
type: boolean type: boolean
description: | description: |
Run the module with Conda using the software specified Run the module with Conda using the software specified
via the `conda` directive via the `conda` directive
- singularity_pull_docker_container: - singularity_pull_docker_container:
type: boolean type: boolean
description: | description: |
Instead of directly downloading Singularity images for use with Singularity, Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead. force the workflow to pull and convert Docker containers instead.
input: input:
- meta: - meta:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- vcf: - vcf:
type: file type: file
description: VCF text file description: VCF text file
output: output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf: - vcf:
type: file type: file
description: Output compressed VCF file description: Output compressed VCF file
pattern: "*.{vcf}" pattern: "*.{vcf}"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version
pattern: "*.{version.txt}" pattern: "*.{version.txt}"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

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

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