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Supported Tool

Windowed Adaptive Trimming for FastQ files using quality


The Sickle module parses standard error generated by Sickle, a windowed Adaptive Trimming for fastq files using quality. StdOut can be captured by directing it to a file e.g. sickle command 2> sickle_out.log

The module generates the sample names based on the filenames.

File search patterns

  contents_re: "FastQ \\w*\\s?records kept: .*"
  num_lines: 2