diff --git a/software/bcftools/bgzip/meta.yml b/software/bcftools/bgzip/meta.yml new file mode 100644 index 00000000..21424516 --- /dev/null +++ b/software/bcftools/bgzip/meta.yml @@ -0,0 +1,75 @@ +name: bcftoos_ +description: foo +keywords: + - align + - fasta + - genome + - reference +tools: + - bowtie2: + description: | + BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1038/nmeth.1923 +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. + - 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. + - save_unaligned: + type: boolean + description: Save unaligned reads +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: file + description: Bowtie2 genome index files + pattern: "*.ebwt" +output: + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - log: + type: file + description: Aligment log + pattern: "*.log" +authors: + - "@kevinmenden" + - "@joseespinosa" + - "@drpatelh" diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml index e4330967..c25b862a 100644 --- a/software/bowtie2/build/meta.yml +++ b/software/bowtie2/build/meta.yml @@ -49,6 +49,5 @@ output: description: File containing software version pattern: "*.{version.txt}" authors: - - "@kevinmenden" - "@joseespinosa" - "drpatelh"