From eb12f4610dd0f04c55f76db9a7e4f0e6e8d4073f Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 1 Feb 2021 09:28:51 +0100 Subject: [PATCH] Fixing meta ymls --- software/bcftools/bgzip/meta.yml | 71 ++++++++++++++------------- software/bcftools/consensus/meta.yml | 73 +++++++++++++++------------- 2 files changed, 77 insertions(+), 67 deletions(-) diff --git a/software/bcftools/bgzip/meta.yml b/software/bcftools/bgzip/meta.yml index b0803961..c2f9e548 100644 --- a/software/bcftools/bgzip/meta.yml +++ b/software/bcftools/bgzip/meta.yml @@ -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 `$params.outdir/` + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` - 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" diff --git a/software/bcftools/consensus/meta.yml b/software/bcftools/consensus/meta.yml index 4f3405f3..658f1ad9 100644 --- a/software/bcftools/consensus/meta.yml +++ b/software/bcftools/consensus/meta.yml @@ -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 `$params.outdir/` + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` - 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"