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59 lines
1.6 KiB
YAML
59 lines
1.6 KiB
YAML
name: umitools_dedup
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description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
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keywords:
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- umitools
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- deduplication
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tools:
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- umi_tools:
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description: >
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UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
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and single cell RNA-Seq cell barcodes
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documentation: https://umi-tools.readthedocs.io/en/latest/
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license: ["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: |
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BAM file containing reads to be deduplicated via UMIs.
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pattern: "*.{bam}"
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- bai:
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type: file
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description: |
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BAM index files corresponding to the input BAM file.
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pattern: "*.{bai}"
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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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- bam:
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type: file
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description: BAM file with deduplicated UMIs.
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pattern: "*.{bam}"
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- tsv_edit_distance:
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type: file
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description: Reports the (binned) average edit distance between the UMIs at each position.
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pattern: "*edit_distance.tsv"
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- tsv_per_umi:
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type: file
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description: UMI-level summary statistics.
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pattern: "*per_umi.tsv"
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- tsv_umi_per_position:
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type: file
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description: Tabulates the counts for unique combinations of UMI and position.
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pattern: "*per_position.tsv"
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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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- "@grst"
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- "@klkeys"
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