[Microarray] Assertion fails in GENERATE_SOFTWARE_TABLE when data files are not compressed

[cyouh95]

Description

R.utils is only used when data files are compressed (e.g., .CEL.gz) to unzip them. The following assertion fails with uncompressed data files (e.g., .CEL) because R.utils is not used:

GeneLab_Data_Processing/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/modules/GENERATE_SOFTWARE_TABLE/resources/usr/bin/SoftwareYamlToMarkdownTable.py

Line 57 in 90d6bb5

assert len(AFFYMETRIX_SOFTWARE_DPPD) == len(df), f"Not all software accounted for! Missing: {set(AFFYMETRIX_SOFTWARE_DPPD) - set(df['name'].str.lower())}"

Solution

Modify AFFYMETRIX_SOFTWARE_DPPD to exclude R.utils if data files are not compressed. Same thing can be done to AGILENT_SOFTWARE_DPPD in Agilent pipeline.

[cyouh95]

Array Data File Name field in runsheet used to determine whether data files are compressed or not. Quoted commas cause issue in splitCsv() as described here, but can be resolved by specifying quote parameter.