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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>
87 lines
2.6 KiB
YAML
87 lines
2.6 KiB
YAML
name: manta_tumoronly
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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.
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keywords:
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- somatic
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- wgs
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- wxs
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- panel
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- vcf
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- structural variants
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- small indels
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tools:
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- manta:
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description: Structural variant and indel caller for mapped sequencing data
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homepage: https://github.com/Illumina/manta
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documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
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tool_dev_url: https://github.com/Illumina/manta
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doi: "10.1093/bioinformatics/btv710"
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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:
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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:
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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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- 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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- candidate_small_indels_vcf:
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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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- candidate_small_indels_vcf_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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- candidate_sv_vcf:
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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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- candidate_sv_vcf_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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- tumor_sv_vcf:
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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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- tumor_sv_vcf_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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- "@maxulysse"
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