fixed rescoring range bugs

[daichengxin]

User description

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• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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PR Type

Bug fix

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Description

• Remove hardcoded qval_score parameter from ID_RIPPER module

• Fix channel mapping in rescoring workflows

• Simplify data flow by removing unnecessary score parameter

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Diagram Walkthrough

flowchart LR
  A["ID_RIPPER module"] --> B["Remove qval_score input/output"]
  B --> C["Update channel mapping"]
  C --> D["Fix DDA_ID workflow"]
  C --> E["Fix PSM_RESCORING workflow"]

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File Walkthrough

Relevant files

Bug fix

main.nf Remove qval_score parameter from ID_RIPPER                              modules/local/openms/id_ripper/main.nf Remove qval_score parameter from input tuple Remove qval_score output emission Simplify module interface +1/-2      main.nf Fix channel mapping in DDA_ID workflow                                      subworkflows/local/dda_id/main.nf Remove hardcoded "MS:1001491" from channel mapping Fix tuple structure in consensus input channel Apply changes to both rescoring range conditions +2/-2      main.nf Fix channel mapping in PSM_RESCORING workflow                        subworkflows/local/psm_rescoring/main.nf Remove hardcoded "MS:1001491" from channel mapping Fix tuple structure in consensus input channel Apply changes to both rescoring range conditions +2/-2

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[qodo-merge-pro]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Interface Change The ID_RIPPER input tuple now expects only (meta, id_file). Validate that upstream channels (e.g., PERCOLATOR outputs) provide exactly two elements to avoid arity mismatches at runtime. tuple val(meta), path(id_file) Channel Tuple Shape ch_consensus_input now carries two items ([meta, id_file]). Confirm that all downstream consumers in DDA_ID expect a pair and not the previous triple, across all branches of the workflow. .map{ [it[1], it[2]]} .set{ ch_consensus_input } Channel Tuple Shape ch_consensus_input was reduced to two items. Ensure any subsequent processes in PSM_RESCORING that consume this channel are updated accordingly. .map{ [it[1], it[2]]} .set{ ch_consensus_input }

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[Copilot]

Pull Request Overview

This PR fixes bugs related to channel mapping and parameter handling in the rescoring workflows. The changes remove a hardcoded qval_score parameter that was causing issues in the data flow between modules.

• Remove hardcoded qval_score parameter from ID_RIPPER module interface
• Fix channel mapping by removing hardcoded "MS:1001491" score parameter from consensus input channels
• Simplify data flow in both DDA_ID and PSM_RESCORING workflows

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
modules/local/openms/id_ripper/main.nf	Removes qval_score parameter from input/output to simplify module interface
subworkflows/local/dda_id/main.nf	Fixes channel mapping by removing hardcoded score parameter in both rescoring conditions
subworkflows/local/psm_rescoring/main.nf	Fixes channel mapping by removing hardcoded score parameter in both rescoring conditions

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