Conditional fastq file finder fix #86
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NuQC uses a helper function that must filter for non-fastq, zero-length, and other undesirable files. Depending on the type of pipeline, undesirables can also include index fastq files. Fix allows I2 files to pass filter if they are found. New test tests for successful pass-through of I1 and I2 files when appropriate, as well as exclusion of zero-length, adapter-trimmed only files, etc.
antgonza
requested changes
Apr 3, 2024
qp_klp/tests/test_step.py
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| @@ -419,6 +426,68 @@ def _create_test_input(self, stage): | |||
| with open(fake_path, 'w') as f: | |||
| f.write("This is a file") | |||
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| if stage >= 5: | |||
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The 5 was so that it wouldn't interfere with legacy tests. Looking at it again there's something I want to tweak. I'll keep you posted.
Consolidated stage numbers 4 -> 3. New stage moved to _create_alternate_test_input() as it's separate and distinct from the other stages.
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NuQC uses a helper function that must filter for non-fastq, zero-length, and other undesirable files. Depending on the type of pipeline, undesirables can also include index fastq files.
Fix allows I2 files to pass filter if they are found. New test tests for successful pass-through of I1 and I2 files when appropriate, as well as exclusion of zero-length, adapter-trimmed only files, etc.