mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
87 lines
2.6 KiB
YAML
87 lines
2.6 KiB
YAML
name: manta_tumoronly
|
|
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:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- input_index:
|
|
type: file
|
|
description: BAM/CRAM/SAM index file
|
|
pattern: "*.{bai,crai,sai}"
|
|
- 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}"
|
|
- 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}"
|
|
|
|
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}"
|
|
- tumor_sv_vcf:
|
|
type: file
|
|
description: Gzipped VCF file containing variants
|
|
pattern: "*.{vcf.gz}"
|
|
- tumor_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:
|
|
- "@maxulysse"
|