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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>
88 lines
2.7 KiB
YAML
88 lines
2.7 KiB
YAML
name: manta_germline
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description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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keywords:
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- somatic
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- wgs
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- wxs
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- panel
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- vcf
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- structural variants
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- small indels
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tools:
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- manta:
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description: Structural variant and indel caller for mapped sequencing data
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homepage: https://github.com/Illumina/manta
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documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
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tool_dev_url: https://github.com/Illumina/manta
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doi: "10.1093/bioinformatics/btv710"
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licence: ["GPL v3"]
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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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- input:
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type: file
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description: BAM/CRAM/SAM file. For joint calling use a list of files.
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pattern: "*.{bam,cram,sam}"
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- index:
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type: file
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description: BAM/CRAM/SAM index file. For joint calling use a list of files.
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pattern: "*.{bai,crai,sai}"
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- fasta:
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type: file
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description: Genome reference FASTA file
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pattern: "*.{fa,fasta}"
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- fasta_fai:
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type: file
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description: Genome reference FASTA index file
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pattern: "*.{fa.fai,fasta.fai}"
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- target_bed:
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type: file
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description: BED file containing target regions for variant calling
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pattern: "*.{bed}"
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- target_bed_tbi:
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type: file
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description: Index for BED file containing target regions for variant calling
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pattern: "*.{bed.tbi}"
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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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- candidate_small_indels_vcf:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- candidate_small_indels_vcf_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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- candidate_sv_vcf:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- candidate_sv_vcf_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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- diploid_sv_vcf:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- diploid_sv_vcf_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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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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- "@maxulysse"
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- "@ramprasadn"
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