Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM file containing reads to be deduplicated via UMIs.
*.{bam}
bai
BAM index files corresponding to the input BAM file.
*.{bai}
get_output_stats
:boolean
Whether or not to generate output stats.
${prefix}.bam
BAM file with deduplicated UMIs.
log
*.log
File with logging information
*.{log}
tsv_edit_distance
*edit_distance.tsv
Reports the (binned) average edit distance between the UMIs at each position.
tsv_per_umi
*per_umi.tsv
UMI-level summary statistics.
tsv_umi_per_position
*per_position.tsv
Tabulates the counts for unique combinations of UMI and position.
versions_umitools
${task.process}
:string
The name of the process
umitools
The name of the tool
umi_tools --version | sed 's/UMI-tools version: //'
:eval
The expression to obtain the version of the tool
versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
