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
input:file
Input bam file
*.bam
bai:file
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
BAM file with deduplicated UMIs.
*.{bam}
fastq
*dedup*fastq.gz:file
FASTQ file with deduplicated UMIs.
*dedup*fastq.gz
log
*_UMICollapse.log:file
A log file with the deduplication statistics.
*_{UMICollapse.log}
versions
versions.yml:file
File containing software versions
versions.yml
UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).
