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Add the Metagenome Assembly (metaassembly) pipeline - #771

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MrCreosote merged 1 commit into
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dev-service
Sep 29, 2026
Merged

MrCreosote merged 1 commit into
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dev-service

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Registers cdmtaskservice/pipelines/metaassembly/v0_1_0.py, wrapping the JGI jgi_metaAssembly WDL (short-read/BBTools+metaSPAdes path only) the same way readsqc wraps rqcfilter. threads is hardcoded to "16" and memory is left unset per the upstream repo's memory_and_threads.md analysis; input_file/input_file2 are exposed as single files, matching the two shapes the short-read WDL path actually handles safely.

Also renames test/pipelines/readsqc/v0_1_0_test.py to readsqc_v0_1_0_test.py so its basename doesn't collide with the new metaassembly_v0_1_0_test.py under pytest's default import mode.

Registers cdmtaskservice/pipelines/metaassembly/v0_1_0.py, wrapping the
JGI jgi_metaAssembly WDL (short-read/BBTools+metaSPAdes path only) the
same way readsqc wraps rqcfilter. threads is hardcoded to "16" and
memory is left unset per the upstream repo's memory_and_threads.md
analysis; input_file/input_file2 are exposed as single files, matching
the two shapes the short-read WDL path actually handles safely.

Also renames test/pipelines/readsqc/v0_1_0_test.py to
readsqc_v0_1_0_test.py so its basename doesn't collide with the new
metaassembly_v0_1_0_test.py under pytest's default import mode.
@codecov

codecov Bot commented Sep 29, 2026

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Codecov Report

❌ Patch coverage is 98.36066% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 65.58%. Comparing base (d55a261) to head (efb1960).
⚠️ Report is 29 commits behind head on main.

Files with missing lines Patch % Lines
cdmtaskservice/app_state.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #771      +/-   ##
==========================================
+ Coverage   65.32%   65.58%   +0.25%     
==========================================
  Files          76       77       +1     
  Lines        7747     7808      +61     
==========================================
+ Hits         5061     5121      +60     
- Misses       2686     2687       +1     

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@MrCreosote
MrCreosote merged commit d1aad38 into main Sep 29, 2026
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