The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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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

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htprocess1 -> sample_input_files

Input File(s)

Use the 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.


  • Default parameters only, no further configuration needed.


Output File(s)

Expect a 2 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

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