bump onsite version#44
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📝 WalkthroughWalkthroughThe ChangesONSITE Dynamic Output Suffix and idXML Support
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Actionable comments posted: 1
🧹 Nitpick comments (1)
modules/bigbio/onsite/main.nf (1)
39-44: 🧹 Nitpick | 🔵 Trivial | ⚡ Quick winConsider refactoring nested ternary operators for readability.
The nested ternary operators work correctly but can be difficult to read and maintain. Consider refactoring to a more explicit if-else structure for better clarity.
♻️ Proposed refactor using if-else statements
- def suffix = id_file.name.endsWith(".idparquet") - ? "idparquet" - : id_file.name.endsWith(".idXML") - ? "idXML" - : id_file.name.endsWith(".mzIdentML") - ? "mzIdentML" : "idparquet" + def suffix = "idparquet" // default fallback + if (id_file.name.endsWith(".idparquet")) { + suffix = "idparquet" + } else if (id_file.name.endsWith(".idXML")) { + suffix = "idXML" + } else if (id_file.name.endsWith(".mzIdentML")) { + suffix = "mzIdentML" + }🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@modules/bigbio/onsite/main.nf` around lines 39 - 44, The nested ternary operators in the suffix variable assignment are difficult to read and maintain. Refactor the suffix assignment to use an explicit if-else structure instead of the nested ternaries. Check each file extension condition (idparquet, idXML, mzIdentML) using if-else statements on the id_file.name property, maintaining the same logic where idparquet is the default fallback when no other extensions match. This will improve code clarity and make it easier to maintain in the future.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@modules/bigbio/onsite/main.nf`:
- Line 14: The main.nf file now emits the ptm_in_id_onsite output with an
expanded glob pattern that includes three file formats (idparquet, idXML, and
mzIdentML), but the meta.yml documentation has not been updated to reflect these
changes. Update the meta.yml file to document all three output file formats that
are now being produced by the ptm_in_id_onsite emit, ensuring the output section
accurately describes the complete set of possible output files from this channel
to maintain consistency between the code and its documentation.
---
Nitpick comments:
In `@modules/bigbio/onsite/main.nf`:
- Around line 39-44: The nested ternary operators in the suffix variable
assignment are difficult to read and maintain. Refactor the suffix assignment to
use an explicit if-else structure instead of the nested ternaries. Check each
file extension condition (idparquet, idXML, mzIdentML) using if-else statements
on the id_file.name property, maintaining the same logic where idparquet is the
default fallback when no other extensions match. This will improve code clarity
and make it easier to maintain in the future.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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📒 Files selected for processing (3)
modules/bigbio/onsite/main.nfmodules/bigbio/onsite/tests/main.nf.testtests/config/test_data.config
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main.nfincludes process definitionmeta.ymlincludes complete documentationenvironment.ymlspecifies dependenciesModule Type
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Summary by CodeRabbit
New Features
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Tests