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 ]
input
:file
Input bam file
*.bam
bai
BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.
*.{bai}
mode
:string
Selects the mode of Umicollapse - either fastq or bam need to be provided.
{fastq,bam}
bam
BAM file with deduplicated UMIs.
*.{bam}
fastq
*dedup*fastq.gz
FASTQ file with deduplicated UMIs.
log
*_UMICollapse.log
A log file with the deduplication statistics.
*_{UMICollapse.log}
versions_umicollapse
${task.process}
The name of the process
umicollapse
The name of the tool
1.1.0-0
:eval
The expression to obtain the version of the tool
versions
UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).
