mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +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>
63 lines
1.7 KiB
YAML
63 lines
1.7 KiB
YAML
name: strelka_germline
|
|
description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
|
|
keywords:
|
|
- variantcalling
|
|
- germline
|
|
- wgs
|
|
- vcf
|
|
- variants
|
|
tools:
|
|
- strelka:
|
|
description: Strelka calls somatic and germline small variants from mapped sequencing reads
|
|
homepage: https://github.com/Illumina/strelka
|
|
documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
|
|
tool_dev_url: https://github.com/Illumina/strelka
|
|
doi: 10.1038/s41592-018-0051-x
|
|
licence: ['GPL v3']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test']
|
|
- input:
|
|
type: file
|
|
description: BAM/CRAM file
|
|
pattern: "*.{bam,cram}"
|
|
- input_index:
|
|
type: file
|
|
description: BAM/CRAI index file
|
|
pattern: "*.{bai,crai}"
|
|
- target_bed:
|
|
type: file
|
|
description: An optional bed file
|
|
pattern: "*.{bed}"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test']
|
|
- vcf:
|
|
type: file
|
|
description: gzipped germline variant file
|
|
pattern: "*.{vcf.gz}"
|
|
- vcf_tbi:
|
|
type: file
|
|
description: index file for the vcf file
|
|
pattern: "*.vcf.gz.tbi"
|
|
- genome_vcf:
|
|
type: file
|
|
description: variant records and compressed non-variant blocks
|
|
pattern: "*_genome.vcf.gz"
|
|
- genome_vcf_tbi:
|
|
type: file
|
|
description: index file for the genome_vcf file
|
|
pattern: "*_genome.vcf.gz.tbi"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@arontommi"
|