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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
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description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
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keywords:
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- variantcalling
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- germline
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- wgs
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- vcf
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- variants
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tools:
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- strelka:
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description: Strelka calls somatic and germline small variants from mapped sequencing reads
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homepage: https://github.com/Illumina/strelka
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documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
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tool_dev_url: https://github.com/Illumina/strelka
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doi: 10.1038/s41592-018-0051-x
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licence: ['GPL v3']
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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']
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- input:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAM/CRAI index file
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pattern: "*.{bai,crai}"
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- target_bed:
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type: file
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description: An optional bed file
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pattern: "*.{bed}"
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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']
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- vcf:
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type: file
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description: gzipped germline variant file
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pattern: "*.{vcf.gz}"
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- vcf_tbi:
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type: file
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description: index file for the vcf file
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pattern: "*.vcf.gz.tbi"
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- genome_vcf:
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type: file
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description: variant records and compressed non-variant blocks
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pattern: "*_genome.vcf.gz"
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- genome_vcf_tbi:
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type: file
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description: index file for the genome_vcf file
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pattern: "*_genome.vcf.gz.tbi"
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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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authors:
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- "@arontommi"
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