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No code changes required to pass testing. May want to write helper functions to abstract over some changes, depending on how other projects use this parser.
Not 100% sure this is the right thing to do - this may be intended to list only modules that are guaranteed to be present. Alternatively, split into EXPECTED and OPTIONAL modules.
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Alas, I just had to change around the files in this repo to make it a proper package--if you could reapply and push back up, I will merge this in and go forward. Also, we'll want to tick the version number up for this, and start to do that EXPECTED/OPTIONAL split so we can do both FastQC v0.10 and v0.11. Once we have the parser working for v0.11, we will be able to start moving our pipeline to use v0.11. |
EXPECTED_MODULES are guaranteed to be present for supported versions of FastQC, OPTIONAL_MODULES may or may not be present.
New features: FastQC version 0.11.2 compatiblity
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Alright, merged in master, split out the three optional modules into |
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The parser already works for FastQC v0.11 data (issue #4). There's 2 modules added, one removed (per-base GC content, which always struck me as redundant), and a few fields renamed (notably, "Filtered" -> "Sequences flagged as poor quality").
I think the LIMS will error with this change, as it's expecting all the modules in EXPECTED_MODULES to be present. It might be better to split this array into EXPECTED/OPTIONAL.