nf-core_modules/modules/umitools/dedup/meta.yml

63 lines
1.7 KiB
YAML

name: umitools_dedup
description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
keywords:
- umitools
- deduplication
tools:
- umi_tools:
description: >
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
and single cell RNA-Seq cell barcodes
documentation: https://umi-tools.readthedocs.io/en/latest/
license: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: |
BAM file containing reads to be deduplicated via UMIs.
pattern: "*.{bam}"
- bai:
type: file
description: |
BAM index files corresponding to the input BAM file.
pattern: "*.{bai}"
- get_output_stats:
type: boolean
description: |
Whether or not to generate output stats.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file with deduplicated UMIs.
pattern: "*.{bam}"
- tsv_edit_distance:
type: file
description: Reports the (binned) average edit distance between the UMIs at each position.
pattern: "*edit_distance.tsv"
- tsv_per_umi:
type: file
description: UMI-level summary statistics.
pattern: "*per_umi.tsv"
- tsv_umi_per_position:
type: file
description: Tabulates the counts for unique combinations of UMI and position.
pattern: "*per_position.tsv"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@grst"
- "@klkeys"