assemblerflow.templates.trimmomatic module

Purpose

This module is intended execute trimmomatic on paired-end FastQ files.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

• fastq_id : Pair of FastQ file paths.

  • e.g.: 'SampleA'

• fastq_pair : Pair of FastQ file paths.

  • e.g.: 'SampleA_1.fastq.gz SampleA_2.fastq.gz'

• trim_range : Crop range detected using FastQC.

  • e.g.: '15 151'

• opts : List of options for trimmomatic

  • e.g.: '["5:20", "3", "3", "55"]'
  • e.g.: '[trim_sliding_window, trim_leading, trim_trailing, trim_min_length]'

• phred : List of guessed phred values for each sample

  • e.g.: '[SampleA: 33, SampleB: 33]'

Generated output

The generated output are output files that contain an object, usually a string. (Values within ${} are substituted by the corresponding variable.)

• ${fastq_id}_*P*: Pair of paired FastQ files generated by Trimmomatic

  • e.g.: 'SampleA_1_P.fastq.gz SampleA_2_P.fastq.gz'

• trimmomatic_status: Stores the status of the trimmomatic run. If it was successfully executed, it stores ‘pass’. Otherwise, it stores the STDERR message.

  • e.g.: 'pass'

Code documentation

assemblerflow.templates.trimmomatic.parse_log(log_file)

Retrieves some statistics from a single Trimmomatic log file.

This function parses Trimmomatic’s log file and stores some trimming statistics in an OrderedDict object. This object contains the following keys:

• clean_len: Total length after trimming.
• total_trim: Total trimmed base pairs.
• total_trim_perc: Total trimmed base pairs in percentage.
• 5trim: Total base pairs trimmed at 5’ end.
• 3trim: Total base pairs trimmed at 3’ end.

Parameters:

log_file : str

Path to trimmomatic log file.

Returns:

x : OrderedDict

Object storing the trimming statistics.

assemblerflow.templates.trimmomatic.write_report(storage_dic, output_file)

Writes a report from multiple samples.

Parameters:

storage_dic : dict or OrderedDict

Storage containing the trimming statistics. See parse_log() for its generation.

output_file : str

Path where the output file will be generated.

assemblerflow.templates.trimmomatic.trimmomatic_log(log_file)

assemblerflow.templates.trimmomatic.clean_up()

Cleans the working directory of unwanted temporary files

assemblerflow.templates.trimmomatic.merge_default_adapters()

Merges the default adapters file in the trimmomatic adapters directory

Returns:

str

Path with the merged adapters file.