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56 lines
1.4 KiB
YAML
56 lines
1.4 KiB
YAML
name: bam_stats_samtools
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description: Produces comprehensive statistics from SAM/BAM/CRAM file
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keywords:
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- statistics
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- counts
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- bam
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- sam
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- cram
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modules:
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- samtools/stats
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- samtools/idxstats
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- samtools/flagstat
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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: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: Index for BAM/CRAM/SAM 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: Reference genome fasta file
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pattern: "*.{fasta,fa}"
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# TODO Update when we decide on a standard for subworkflow docs
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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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- stats:
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type: file
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description: File containing samtools stats output
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pattern: "*.{stats}"
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- flagstat:
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type: file
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description: File containing samtools flagstat output
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pattern: "*.{flagstat}"
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- idxstats:
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type: file
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description: File containing samtools idxstats output
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pattern: "*.{idxstats}"
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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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