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69 lines
2.4 KiB
YAML
69 lines
2.4 KiB
YAML
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name: "gatk4_printsvevidence"
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description: Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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keywords:
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- structural variants
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- gatk4
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ["Apache-2.0"]
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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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- evidence:
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type: file
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description: The evidence file created by CollectSVEvidence
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pattern: "*.{pe,sr,baf,rd}.txt(.gz)"
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- evidence_index:
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type: file
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description: The index of the evidence file created by CollectSVEvidence
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pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi"
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- bed:
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type: file
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description: An optional BED file
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pattern: "*.bed"
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- fasta:
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type: file
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description: An optional 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: An optional reference FASTA file index
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pattern: "*.fai"
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- dict:
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type: file
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description: The mandatory sequence dictionary file
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pattern: "*.dict"
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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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- 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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- printed_evidence:
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type: file
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description: The output file containing the discordant read pairs or the soft clipped reads
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pattern: "*.{pe,sr,baf,rd}.txt.gz"
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- printed_evidence:
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type: file
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description: The index of the output file containing the discordant read pairs or the soft clipped reads
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pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi"
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authors:
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- "@nvnieuwk"
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