mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 22:23:09 +00:00
89 lines
2.9 KiB
YAML
89 lines
2.9 KiB
YAML
|
name: "gatk4_collectsvevidence"
|
||
|
|
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.
|
||
|
|
keywords:
|
||
|
|
- gatk4
|
||
|
|
- collectsvevidence
|
||
|
|
- structural variants
|
||
|
|
- metrics
|
||
|
|
tools:
|
||
|
|
- "gatk4":
|
||
|
|
description: "Genome Analysis Toolkit (GATK4)"
|
||
|
|
homepage: "https://gatk.broadinstitute.org/hc/en-us"
|
||
|
|
documentation: "None"
|
||
|
|
tool_dev_url: "https://github.com/broadinstitute/gatk"
|
||
|
|
doi: "10.1158/1538-7445.AM2017-3590"
|
||
|
|
licence: "['BSD-3-clause']"
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- input:
|
||
|
|
type: file
|
||
|
|
description: BAM/CRAM/SAM file
|
||
|
|
pattern: "*.{bam,cram,sam}"
|
||
|
|
- input_index:
|
||
|
|
type: file
|
||
|
|
description: Index of the BAM/CRAM/SAM file
|
||
|
|
pattern: "*.{bai,crai,sai}"
|
||
|
|
- allele_count_vcf:
|
||
|
|
type: file
|
||
|
|
description: Optional - input VCF of SNPs marking loci for allele counts, needed for the allele counts output
|
||
|
|
pattern: "*.vcf.gz"
|
||
|
|
- allele_count_vcf_index:
|
||
|
|
type: file
|
||
|
|
description: Optional - index of the VCF file, needed for the allele counts output
|
||
|
|
pattern: "*.tbi"
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: Optional - reference FASTA file needed when the input is a CRAM file
|
||
|
|
pattern: "*.{fasta,fa}"
|
||
|
|
- fasta_fai:
|
||
|
|
type: file
|
||
|
|
description: Optional - index of the reference FASTA file needed when the input is a CRAM file
|
||
|
|
pattern: "*.fai"
|
||
|
|
- dict:
|
||
|
|
type: file
|
||
|
|
description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file
|
||
|
|
pattern: "*.dict"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
- split_read_evidence:
|
||
|
|
type: file
|
||
|
|
description: Output file for split read evidence
|
||
|
|
pattern: "*.sr.txt.gz"
|
||
|
|
- split_read_evidence_index:
|
||
|
|
type: file
|
||
|
|
description: Index of the output file for split read evidence
|
||
|
|
pattern: "*.sr.txt.gz.tbi"
|
||
|
|
- paired_end_evidence:
|
||
|
|
type: file
|
||
|
|
description: Output file for paired end evidence
|
||
|
|
pattern: "*.pe.txt.gz"
|
||
|
|
- paired_end_evidence_index:
|
||
|
|
type: file
|
||
|
|
description: Index of the output file for paired end evidence
|
||
|
|
pattern: "*.pe.txt.gz.tbi"
|
||
|
|
- allele_counts:
|
||
|
|
type: file
|
||
|
|
description: Output file for allele counts
|
||
|
|
pattern: "*.ld.txt.gz"
|
||
|
|
- allele_counts_index:
|
||
|
|
type: file
|
||
|
|
description: Index of the output file for allele counts
|
||
|
|
pattern: "*.ld.txt.gz.tbi"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@nvnieuwk"
|