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99 lines
2.9 KiB
YAML
99 lines
2.9 KiB
YAML
name: mosdepth
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description: Calculates genome-wide sequencing coverage.
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keywords:
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- mosdepth
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- bam
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- cram
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- coverage
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tools:
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- mosdepth:
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description: |
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Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
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documentation: https://github.com/brentp/mosdepth
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doi: 10.1093/bioinformatics/btx699
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licence: ["MIT"]
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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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- bam:
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type: file
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description: Input BAM/CRAM file
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pattern: "*.{bam,cram}"
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- bai:
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type: file
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description: Index for BAM/CRAM file
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pattern: "*.{bai,crai}"
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- bed:
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type: file
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description: BED file with intersected intervals
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pattern: "*.{bed}"
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- fasta:
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type: file
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description: Reference genome FASTA file
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pattern: "*.{fa,fasta}"
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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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- global_txt:
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type: file
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description: Text file with global cumulative coverage distribution
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pattern: "*.{global.dist.txt}"
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- regions_txt:
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type: file
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description: Text file with region cumulative coverage distribution
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pattern: "*.{region.dist.txt}"
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- summary_txt:
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type: file
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description: Text file with summary mean depths per chromosome and regions
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pattern: "*.{summary.txt}"
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- per_base_bed:
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type: file
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description: BED file with per-base coverage
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pattern: "*.{per-base.bed.gz}"
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- per_base_csi:
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type: file
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description: Index file for BED file with per-base coverage
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pattern: "*.{per-base.bed.gz.csi}"
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- per_base_d4:
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type: file
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description: D4 file with per-base coverage
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pattern: "*.{per-base.d4}"
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- regions_bed:
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type: file
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description: BED file with per-region coverage
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pattern: "*.{regions.bed.gz}"
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- regions_csi:
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type: file
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description: Index file for BED file with per-region coverage
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pattern: "*.{regions.bed.gz.csi}"
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- quantized_bed:
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type: file
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description: BED file with binned coverage
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pattern: "*.{quantized.bed.gz}"
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- quantized_csi:
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type: file
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description: Index file for BED file with binned coverage
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pattern: "*.{quantized.bed.gz.csi}"
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- thresholds_bed:
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type: file
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description: BED file with the number of bases in each region that are covered at or above each threshold
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pattern: "*.{thresholds.bed.gz}"
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- thresholds_csi:
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type: file
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description: Index file for BED file with threshold coverage
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pattern: "*.{thresholds.bed.gz.csi}"
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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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- "@joseespinosa"
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- "@drpatelh"
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- "@ramprasadn"
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- "@matthdsm"
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