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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
1.4 KiB
YAML
57 lines
1.4 KiB
YAML
name: bcftools_mpileup
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description: Compresses VCF files
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keywords:
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- variant calling
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- mpileup
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- VCF
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tools:
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- mpileup:
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description: |
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Generates genotype likelihoods at each genomic position with coverage.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: Input BAM file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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- save_mpileup:
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type: boolean
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description: Save mpileup file generated by bcftools mpileup
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patter: "*.mpileup"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: VCF gzipped output file
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pattern: "*.{vcf.gz}"
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- tbi:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- stats:
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type: file
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description: Text output file containing stats
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pattern: "*{stats.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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