bump quantms-rescoring version - fix bug with quantms-rescoring container permissions

[daichengxin]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the bigbio/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
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[qodo-code-review]

Review Summary by Qodo

Upgrade quantms-rescoring to 0.0.15 and remove environment setup code

✨ Enhancement

Walkthroughs

Description

• Upgrade quantms-rescoring container images to version 0.0.15
• Remove redundant UID/environment variable setup code from processes
• Simplify container initialization across four rescoring modules

Diagram

flowchart LR
  A["Four Rescoring Modules"] -->|"Update container version"| B["0.0.15 Images"]
  A -->|"Remove UID setup code"| C["Simplified Scripts"]
  B --> D["Enhanced Processes"]
  C --> D

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File Changes

1. modules/local/utils/msrescore_features/main.nf ✨ Enhancement +2/-16

Update msrescore_features container and remove setup code

• Updated container image version from 0.0.14 to 0.0.15
• Removed 15-line UID-less environment setup block
• Simplified script initialization for feature extraction

modules/local/utils/msrescore_features/main.nf

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2. modules/local/utils/msrescore_fine_tuning/main.nf ✨ Enhancement +2/-13

Update msrescore_fine_tuning container and remove setup code

• Updated container image version from 0.0.14 to 0.0.15
• Removed 14-line UID-less container environment setup block
• Streamlined transfer learning process initialization

modules/local/utils/msrescore_fine_tuning/main.nf

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3. modules/local/utils/psm_clean/main.nf ✨ Enhancement +2/-12

Update psm_clean container and remove setup code

• Updated container image version from 0.0.13 to 0.0.15
• Removed 13-line UID-less container environment setup block
• Simplified PSM cleaning process initialization

modules/local/utils/psm_clean/main.nf

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View more (1)

4. modules/local/utils/spectrum_features/main.nf ✨ Enhancement +2/-12

Update spectrum_features container and remove setup code

• Updated container image version from 0.0.13 to 0.0.15
• Removed 13-line UID-less container environment setup block
• Simplified spectrum feature extraction initialization

modules/local/utils/spectrum_features/main.nf

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[qodo-code-review]

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (0) 📎 Requirement gaps (0)

1. Removed UID/HOME hardening 🐞 Bug ⛯ Reliability

Description

The PR removes per-process environment setup (USER/LOGNAME/HOME and cache dir prep) from several
quantms-rescoring steps. With the pipeline’s Docker profile forcing containers to run as the host
UID/GID, this can break in arbitrary-UID environments (no passwd entry, non-existent or non-writable
$HOME), causing rescoring steps to fail at runtime.

Code

modules/local/utils/msrescore_fine_tuning/main.nf[L51-61]

-    # Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
-    # Python's getpass.getuser() checks USER env var before calling getpwuid()
-    if [ -w /etc/passwd ]; then
-        echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
-    fi
-    export USER="\${USER:-quantms}"
-    export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
-    export HOME="\${HOME:-\$PWD}"
-    export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
-    mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"
-

Evidence

The pipeline explicitly runs Docker containers as the host UID/GID, which commonly results in a UID
that is not present in the container’s /etc/passwd and may not have a valid/writable home directory.
After this PR, the rescoring processes execute rescoring ... directly without setting USER/HOME
(or a writable cache location). These processes are part of the main peptide DB search subworkflow
when rescoring/MS2 features are enabled, so failures would block that workflow branch.

nextflow.config[302-311]
modules/local/utils/msrescore_fine_tuning/main.nf[50-66]
modules/local/utils/msrescore_features/main.nf[93-108]
modules/local/utils/psm_clean/main.nf[24-31]
modules/local/utils/spectrum_features/main.nf[21-28]
subworkflows/local/peptide_database_search/main.nf[6-12]
subworkflows/local/peptide_database_search/main.nf[77-169]
modules/local/utils/msrescore_fine_tuning/meta.yml[1-3]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
The rescoring-related modules no longer set `USER`/`LOGNAME`/`HOME` (and previously prepared a writable cache dir). This is risky because the default `docker` profile runs containers with `-u $(id -u):$(id -g)`, which can yield an arbitrary UID inside the container with no passwd entry and/or no valid writable home directory.

### Issue Context
These processes (`MSRESCORE_FEATURES`, `MSRESCORE_FINE_TUNING`, `PSM_CLEAN`, `SPECTRUM_FEATURES`) are invoked from the peptide database search subworkflow when MS2 features/rescoring is enabled.

### Fix Focus Areas
- modules/local/utils/msrescore_features/main.nf[93-108]
- modules/local/utils/msrescore_fine_tuning/main.nf[50-66]
- modules/local/utils/psm_clean/main.nf[24-31]
- modules/local/utils/spectrum_features/main.nf[21-28]

Suggested implementation pattern (apply at the top of each script block, before calling `rescoring ...`):
- `export USER="${USER:-quantms}"`
- `export LOGNAME="${LOGNAME:-$USER}"`
- `export HOME="${HOME:-$PWD}"`
- (optional) `export XDG_CACHE_HOME="${XDG_CACHE_HOME:-$PWD/.cache}"; mkdir -p "$XDG_CACHE_HOME"`
- (optional, only if needed) `export TORCHINDUCTOR_CACHE_DIR="${TORCHINDUCTOR_CACHE_DIR:-$PWD/.torchinductor_cache}"; mkdir -p "$TORCHINDUCTOR_CACHE_DIR"`

If the container image v0.0.15 now guarantees correct behavior without this bootstrap, add/ensure a CI test profile that runs these steps under arbitrary UID and document that assumption in-code to prevent future regressions.

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[jpfeuffer]

Much better! Can you link the upstream fix PR please?

[daichengxin]

Fix PR bigbio/quantms-rescoring#64

[ypriverol]

Also for tracing @daichengxin and @jpfeuffer, this PR tackles the following issue: #678