Add trim_galore test fixtures (for MultiQC#3538)#377
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FelixKrueger wants to merge 1 commit intoMultiQC:mainfrom
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Add trim_galore test fixtures (for MultiQC#3538)#377FelixKrueger wants to merge 1 commit intoMultiQC:mainfrom
FelixKrueger wants to merge 1 commit intoMultiQC:mainfrom
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Test fixtures for the new MultiQC `trim_galore` module proposed in MultiQC/MultiQC#3538. These are real Trim Galore v2.1.0-beta.5 outputs: - sample_R1.fastq.gz_trimming_report.json — single-end (10K Illumina, long adapter-length distribution including the 1-bp tail typical for --stringency 1 default) - BS-seq_10K_R{1,2}.fastq.gz_trimming_report.json — paired-end pair (BS-seq 10K, with `pair_validation` populated and short adapter-length tails — useful coverage for the PE code path) Schema reference: schema_version 1, documented in the upstream issue thread at MultiQC/MultiQC#3529.
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The fixtures originally landed in `tests/data/modules/trim_galore/` of the main repo, but `test_modules_run.py` resolves test data via `<repo>/test-data/data/modules/<module>/` (a separate sibling repo, MultiQC/test-data). Moving them there in MultiQC/test-data#377.
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Companion PR to MultiQC/MultiQC#3538, which adds a native MultiQC module for Trim Galore v2.x (closes MultiQC/MultiQC#3529).
This PR drops the test fixtures the new module needs into
data/modules/trim_galore/. Real Trim Galore v2.1.0-beta.5 JSON outputs:sample_R1.fastq.gz_trimming_report.json— single-end (10K Illumina, long adapter-length distribution including the 1-bp tail typical for the default--stringency 1)BS-seq_10K_R{1,2}.fastq.gz_trimming_report.json— paired-end pair (BS-seq 10K, withpair_validationpopulated and short adapter-length tails — covers the PE code path)Schema reference:
schema_version: 1, documented in the upstream MultiQC issue thread.The MultiQC PR's
test_modules_run.py::test_all_modules[trim_galore-…]andtest_ignore_samples[trim_galore-…]checks fail until this PR merges (they look fortest-data/data/modules/trim_galore/). Happy to coordinate merge order — most natural is to merge this first, then unblock the MultiQC PR's CI.