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HTProcess-prepare input directories

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Arranges input files in directories for use with HTProcess-fastqc. Intended largely to be used as part of the Discovery Environment Workflow: HTProcess-prepare_directories_and_run_fastqc 0.2.

Quick Start

• To use HTProcess-prepare input directories, import your data in ___ fastq format.
• Resources: http://replace.with.URL.for.tool.documentation.from.the.tool.source.org Cleaning up your reads with the HTProcess Pipeline

Test Data

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from the directory above as test inputthe fastq files from the forward reads directory for the first box, and the fastq files from the reverse reads directory for the second box – find the reads and their directories in the directory above.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note. 

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
  • parameter name - value/setting
  • parameter name - value/setting

Output File(s)

Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt2 directories named paired_reads1 and paired_reads2 as output. If single reads were used, too, a single_reads directory would also be produced.

Tool Source for App

• http://replace.with.URL.for.tool.orgCleaning up your reads with the HTProcess Pipeline