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https://github.com/MillironX/nf-core_modules.git
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89 lines
2.9 KiB
YAML
89 lines
2.9 KiB
YAML
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name: "gatk4_collectsvevidence"
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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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- gatk4
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- collectsvevidence
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- structural variants
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- metrics
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tools:
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- "gatk4":
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description: "Genome Analysis Toolkit (GATK4)"
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homepage: "https://gatk.broadinstitute.org/hc/en-us"
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documentation: "None"
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tool_dev_url: "https://github.com/broadinstitute/gatk"
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doi: "10.1158/1538-7445.AM2017-3590"
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licence: "['BSD-3-clause']"
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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
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pattern: "*.{bam,cram,sam}"
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- input_index:
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type: file
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description: Index of the BAM/CRAM/SAM file
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pattern: "*.{bai,crai,sai}"
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- allele_count_vcf:
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type: file
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description: Optional - input VCF of SNPs marking loci for allele counts, needed for the allele counts output
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pattern: "*.vcf.gz"
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- allele_count_vcf_index:
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type: file
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description: Optional - index of the VCF file, needed for the allele counts output
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pattern: "*.tbi"
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- fasta:
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type: file
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description: Optional - reference FASTA file needed when the input is a CRAM file
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pattern: "*.{fasta,fa}"
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- fasta_fai:
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type: file
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description: Optional - index of the reference FASTA file needed when the input is a CRAM file
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pattern: "*.fai"
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- dict:
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type: file
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description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM 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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- split_read_evidence:
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type: file
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description: Output file for split read evidence
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pattern: "*.sr.txt.gz"
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- split_read_evidence_index:
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type: file
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description: Index of the output file for split read evidence
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pattern: "*.sr.txt.gz.tbi"
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- paired_end_evidence:
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type: file
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description: Output file for paired end evidence
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pattern: "*.pe.txt.gz"
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- paired_end_evidence_index:
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type: file
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description: Index of the output file for paired end evidence
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pattern: "*.pe.txt.gz.tbi"
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- allele_counts:
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type: file
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description: Output file for allele counts
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pattern: "*.ld.txt.gz"
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- allele_counts_index:
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type: file
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description: Index of the output file for allele counts
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pattern: "*.ld.txt.gz.tbi"
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authors:
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- "@nvnieuwk"
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