I have pre-normalized data and want to start my analysis at the DE miRNA module. I created my own table of read counts as shown in the documentation.

The module ran "successfully" but no output was generated. After digging through the code a bit, I found that the module is looking for a specific file name: $projectdir.$output_dir.$name.".tab

However this naming convention isn't mentioned in the documentation, and I originally named my tabular file something else. I believe the correct behaviour should be for the module to fail if the expected file does not exist (preferably with a statement about the naming convention), and not exit successfully.

Script output shown below and config file used is attached.

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miARma, miRNA and RNASeq Multiprocess Analysis

miARma v 1.5 (Apr-2016)

Created at Computational Biology and Bioinformatics Group (CbBio)

Institute of Biomedicine of Seville. IBIS (Spain)

mail : miARma-devel@cbbio.es

[Mon Sep 5 19:13:22 2016] Starting a miARma analysis for miRNA [Mon Sep 5 19:13:22 2016] Checking provided parameters for: DEAnalysis. [Mon Sep 5 19:13:22 2016] Checking General-output_dir parameter ... Exists! [Mon Sep 5 19:13:22 2016] The folder specified in (output_dir=/cluster3_dea/results/) already exists. [Mon Sep 5 19:13:22 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Mon Sep 5 19:13:28 2016] Continue. [Mon Sep 5 19:13:28 2016] All parameters are correct. [Mon Sep 5 19:13:28 2016] Starting a differential expression analysis using edger software(s) [Mon Sep 5 19:13:28 2016] Differential expression analysis finished. [Mon Sep 5 19:13:28 2016] miARma finished. Job took 0 minutes miARma@Ubuntu:~/miARma$

Running DE module with unknowingly incorrectly named table file