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https://github.com/MillironX/nf-core_modules.git
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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>
93 lines
2.7 KiB
YAML
93 lines
2.7 KiB
YAML
name: strelka_somatic
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description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
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keywords:
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- variant calling
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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', single_end:false ]
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- input_normal:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- input_index_normal:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- input_tumor:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- input_index_tumor:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- manta_candidate_small_indels:
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type: file
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description: VCF.gz file
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pattern: "*.{vcf.gz}"
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- manta_candidate_small_indels_tbi:
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type: file
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description: VCF.gz index file
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pattern: "*.tbi"
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- fasta:
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type: file
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description: Genome reference FASTA file
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pattern: "*.{fa,fasta}"
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- fai:
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type: file
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description: Genome reference FASTA index file
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pattern: "*.{fa.fai,fasta.fai}"
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- target_bed:
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type: file
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description: BED file containing target regions for variant calling
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pattern: "*.{bed}"
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- target_bed_tbi:
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type: file
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description: Index for BED file containing target regions for variant calling
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pattern: "*.{bed.tbi}"
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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', single_end:false ]
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- vcf_indels:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- vcf_indels_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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- vcf_snvs:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- vcf_snvs_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{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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- "@drpatelh"
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