nf-core_modules/modules/manta/somatic/meta.yml
nickhsmith 979e57b7ac
Manta consistancy (#1407)
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai)

* update tests

* fix typos

* fix typos

Co-authored-by: Smith Nicholas <smith@in.tum.de>
2022-03-18 13:30:03 +01:00

103 lines
3.1 KiB
YAML

name: manta_somatic
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.
keywords:
- somatic
- wgs
- wxs
- panel
- vcf
- structural variants
- small indels
tools:
- manta:
description: Structural variant and indel caller for mapped sequencing data
homepage: https://github.com/Illumina/manta
documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
tool_dev_url: https://github.com/Illumina/manta
doi: "10.1093/bioinformatics/btv710"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index_normal:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index_tumor:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
pattern: "*.{bed}"
- target_bed_tbi:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- candidate_small_indels_vcf:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- candidate_small_indels_vcf_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- candidate_sv_vcf:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- candidate_sv_vcf_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- diploid_sv_vcf:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- diploid_sv_vcf_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- somatic_sv_vcf:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- somatic_sv_vcf_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@FriederikeHanssen"