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UMICollapse

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

https://github.com/Daniel-Liu-c0deb0t/UMICollapse

Sample names are extracted from log files if possible. In logs, the command line arguments are printed, which must have both the input and output file paths.

umicollapse bam -i SRR19887568.sorted.bam -o SRR19887568.umi_dedup.sorted.bam
Arguments   [bam, -i, SRR19887568.sorted.bam, -o, SRR19887568.umi_dedup.sorted.bam]

umicollapse requires both -i and -o flags as valid file paths. Process substitution is not supported currently by umicollapse, but in case it is used for the -i flag, we fallback to the log file name.

File search patterns​

umicollapse:
  contents: "UMI collapsing finished in "
  num_lines: 100