Repository navigation
Add the Metagenome Assembly (metaassembly) pipeline - #771
Merged
Merged
Conversation
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 Report❌ Patch coverage is
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 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.