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Modify main.nf to match the original version #21

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182d4ef
Modify main.nf to match the original version.
weizhongchun Dec 31, 2025
aac78f1
Update main.nf
weizhongchun Dec 31, 2025
46c5323
Update meta.yml
weizhongchun Dec 31, 2025
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55 changes: 29 additions & 26 deletions modules/bigbio/pmultiqc/main.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
process PMULTIQC {
tag "$meta.id"
label 'process_high'

conda "${moduleDir}/environment.yml"
Expand All @@ -8,42 +7,46 @@ process PMULTIQC {
'biocontainers/pmultiqc:0.0.39--pyhdfd78af_0' }"

input:
val meta
path results
path 'results/*'
path quantms_log
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⚠️ Potential issue | 🟡 Minor

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Search for any usage of quantms_log in the codebase
rg -n 'quantms_log' --type=nf

Repository: bigbio/nf-modules

Length of output: 87

🏁 Script executed:

#!/bin/bash
# Read the main.nf file to see the full context
cat -n modules/bigbio/pmultiqc/main.nf | head -60

Repository: bigbio/nf-modules

Length of output: 2055

🏁 Script executed:

#!/bin/bash
# Search for similar wildcard input patterns in other Nextflow modules
rg "path\s+'[^']+/\*'" --type=nf -A 2

Repository: bigbio/nf-modules

Length of output: 87

🏁 Script executed:

#!/bin/bash
# Search for quantms_log usage without file type restriction
rg 'quantms_log' -n

Repository: bigbio/nf-modules

Length of output: 116

🏁 Script executed:

#!/bin/bash
# Search for wildcard path patterns in Nextflow files
rg "path\s+'" -n | grep -E "\*'|/\*'" | head -20

Repository: bigbio/nf-modules

Length of output: 115

🏁 Script executed:

#!/bin/bash
# Check the broader context of the PR to understand the change
git log --oneline -10 -- modules/bigbio/pmultiqc/main.nf

Repository: bigbio/nf-modules

Length of output: 114

Remove the unused quantms_log input and clarify the wildcard staging pattern.

The quantms_log input is declared at line 10 but is never referenced in the script—it's dead code and should be removed.

The wildcard pattern path 'results/*' is unusual for Nextflow inputs. This is the only occurrence of this pattern in the codebase. Clarify whether this is intentional (to stage individual files into a results/ subdirectory) or if it should be path 'results' to stage the directory itself. The script logic at line 32 (cat results/*openms_design.tsv) and line 43 (./results) suggests the latter is expected.

🤖 Prompt for AI Agents 
In modules/bigbio/pmultiqc/main.nf around lines 9–10, remove the unused
`quantms_log` input declaration and change the unusual `path 'results/*'`
staging pattern to `path 'results'` so the whole directory is staged (this
matches downstream uses like `cat results/*openms_design.tsv` and executing
`./results`); update any tests or documentation if they relied on per-file
staging and run the pipeline to confirm file paths still resolve.


output:
tuple val(meta), path("*.html"), emit: report
path "*.db", optional: true, emit: quantmsdb
path "*.html", emit: ch_pmultiqc_report
path "*.db", optional: true, emit: ch_pmultiqc_db
path "versions.yml", emit: versions
path "*_data", emit: data

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "--quantms_plugin" : ""
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🛠️ Refactor suggestion | 🟠 Major

Misleading variable name.

The variable disable_pmultiqc actually enables the quantms plugin when conditions are met, making the code confusing to maintain. Consider renaming to better reflect its purpose.

🔎 Proposed fix 
-def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "--quantms_plugin" : ""
+def enable_quantms_plugin = (params.enable_pmultiqc) && (params.export_mztab) ? "--quantms_plugin" : ""

And update line 36 accordingly:

-    ${disable_pmultiqc} \\
+    ${enable_quantms_plugin} \\

Committable suggestion skipped: line range outside the PR's diff.

🤖 Prompt for AI Agents 
In modules/bigbio/pmultiqc/main.nf around line 20, the variable name
`disable_pmultiqc` is misleading because it actually sets the quantms plugin
flag when enabled; rename it to something clear like `pmultiqc_quantms_flag` (or
`enable_pmultiqc_quantms`) and update all usages (notably the reference at line
36) to use the new name so the variable meaning matches its behavior; keep the
ternary expression and value unchanged, only rename the identifier and adjust
any downstream references accordingly.

def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable_table" : ""
def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored_idxml" : ""
def contaminant_affix = params.contaminant_string ? "--contaminant_affix ${params.contaminant_string}" : ""

"""
multiqc \\
--force \\
--filename ${prefix}_multiqc_report \\
${args} \\
.
set -x
set -e

cat <<END_VERSIONS > versions.yml
"PMULTIQC":
pmultiqc: \$(python -c "from importlib.metadata import version; print(version('pmultiqc'))" 2>/dev/null || echo "0.0.39")
END_VERSIONS
"""
# leaving here to ease debugging
ls -lcth *

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
cat results/*openms_design.tsv
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⚠️ Potential issue | 🟠 Major

Risk of script failure and debug artifacts.

Two concerns:

  1. Line 32: The cat results/*openms_design.tsv command will fail if the file doesn't exist. Combined with set -e (line 27), this will halt execution. Consider adding existence checks or making this command optional.

  2. Lines 29-30, 32: Debug commands (ls and cat) are left in production code. While the comment indicates they're for debugging, consider removing them or making them conditional on a debug flag.

🔎 Proposed fix for safer file handling 
-cat results/*openms_design.tsv
+if ls results/*openms_design.tsv 1> /dev/null 2>&1; then
+    cat results/*openms_design.tsv
+fi
🤖 Prompt for AI Agents 
In modules/bigbio/pmultiqc/main.nf around lines 26 to 32, the script uses set -e
and includes unconditional debug commands (ls -lcth * and cat
results/*openms_design.tsv) which will either leak debug artifacts in production
or cause the job to fail if the target file is missing; replace these with
conditional checks and a debug flag: add a DEBUG environment variable or
Nextflow parameter that when true runs the ls and cat for debugging, and guard
the cat with an existence check (e.g., test -f results/*openms_design.tsv or
iterate files) or append || true to avoid exiting under set -e when the file is
absent, ensuring production runs don't fail or print debug output unless
explicitly requested.


"""
touch '${prefix}_multiqc_report.html'
mkdir '${prefix}_multiqc_report_data'

cat <<END_VERSIONS > versions.yml
"PMULTIQC":
pmultiqc: \$(python -c "from importlib.metadata import version; print(version('pmultiqc'))" 2>/dev/null || echo "0.0.39")
END_VERSIONS
multiqc \\
-f \\
${disable_pmultiqc} \\
--config ./results/multiqc_config.yml \\
${args} \\
${disable_table_plots} \\
${disable_idxml_index} \\
${contaminant_affix} \\
--quantification_method $params.quantification_method \\
./results \\
-o .
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⚠️ Potential issue | 🟡 Minor

🧩 Analysis chain

🏁 Script executed:

# First, find the file and read it to understand the context around lines 34-44
find . -name "main.nf" -path "*/pmultiqc/*" | head -5

Repository: bigbio/nf-modules

Length of output: 94

🏁 Script executed:

# Search for the pmultiqc module
fd -p "pmultiqc" -t d | head -10

Repository: bigbio/nf-modules

Length of output: 116

🏁 Script executed:

# Read the main.nf file to see full context
cat -n ./modules/bigbio/pmultiqc/main.nf

Repository: bigbio/nf-modules

Length of output: 2055

🏁 Script executed:

# Search for quantification_method parameter in config files
rg -n 'quantification_method' --type=nf -g '*.config' -g 'nextflow.config'

Repository: bigbio/nf-modules

Length of output: 87

🏁 Script executed:

# Also search in all files to understand where this parameter is defined
rg -n 'quantification_method' --max-count=20

Repository: bigbio/nf-modules

Length of output: 298

🏁 Script executed:

# Read the meta.yml to understand the parameter better
cat -n ./modules/bigbio/pmultiqc/meta.yml

Repository: bigbio/nf-modules

Length of output: 2443

🏁 Script executed:

# Search for nextflow.config files to see if quantification_method is defined there
fd -n 'nextflow.config' -o 'config.nf' | head -10

Repository: bigbio/nf-modules

Length of output: 291

🏁 Script executed:

# Search for where this parameter might be defined as a workflow parameter
rg -n 'params\.' -g 'nextflow.config' -g '*.config' | grep -i 'quantification' | head -20

Repository: bigbio/nf-modules

Length of output: 43

🏁 Script executed:

# Find all config files
fd 'nextflow.config' -o '\.config$'

Repository: bigbio/nf-modules

Length of output: 198

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# Check the tests directory for pmultiqc to see how it's configured
find ./modules/bigbio/pmultiqc/tests -type f | head -20

Repository: bigbio/nf-modules

Length of output: 364

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# Look for where quantification_method might be set with a default
rg 'quantification_method\s*=' -B2 -A2

Repository: bigbio/nf-modules

Length of output: 43

🏁 Script executed:

# Read the test nextflow.config files to see how parameters are set
cat -n ./modules/bigbio/pmultiqc/tests/nextflow.config

Repository: bigbio/nf-modules

Length of output: 335

🏁 Script executed:

# Read the quantms variant config
cat -n ./modules/bigbio/pmultiqc/tests/nextflow.config.quantms

Repository: bigbio/nf-modules

Length of output: 427

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# Check if multiqc_config.yml exists in tests
cat -n ./modules/bigbio/pmultiqc/tests/multiqc_config.yml | head -30

Repository: bigbio/nf-modules

Length of output: 149

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# Read the base test config to see if quantification_method is defined
cat -n ./tests/config/nextflow.config

Repository: bigbio/nf-modules

Length of output: 1737

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# Check if there's test_data.config that might define parameters
cat -n ./tests/config/test_data.config | head -50

Repository: bigbio/nf-modules

Length of output: 1875

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# Read the test file to understand how PMULTIQC is invoked
cat -n ./modules/bigbio/pmultiqc/tests/main.nf.test | head -80

Repository: bigbio/nf-modules

Length of output: 3634

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# Continue reading the test file to see if quantification_method is set somewhere
tail -n +50 ./modules/bigbio/pmultiqc/tests/main.nf.test | head -100

Repository: bigbio/nf-modules

Length of output: 3766

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# Search for any default value for quantification_method in the entire codebase
rg 'quantification_method' -B3 -A3

Repository: bigbio/nf-modules

Length of output: 1104

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# Check if there's a default value set anywhere by looking more broadly
rg 'params\.' ./modules/bigbio/pmultiqc/main.nf -A1 -B1

Repository: bigbio/nf-modules

Length of output: 653

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# Check for any conditional usage of quantification_method
rg -C5 'quantification_method' ./modules/bigbio/pmultiqc/main.nf

Repository: bigbio/nf-modules

Length of output: 390

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# Look for parent workflows that might define quantification_method
fd 'workflow.nf' | head -10

Repository: bigbio/nf-modules

Length of output: 43

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# Check if there are any parent configs or if this module is part of a larger workflow
find . -maxdepth 2 -name 'nextflow.config' -type f

Repository: bigbio/nf-modules

Length of output: 43

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# Look at the test more carefully - especially what parameters might be passed
tail -n +100 ./modules/bigbio/pmultiqc/tests/main.nf.test | head -50

Repository: bigbio/nf-modules

Length of output: 1894

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# Check the entire test file to see if there's a quantms_plugin test that would set quantification_method
wc -l ./modules/bigbio/pmultiqc/tests/main.nf.test

Repository: bigbio/nf-modules

Length of output: 109

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# Look at the rest of the test file, particularly the quantms test
tail -n 100 ./modules/bigbio/pmultiqc/tests/main.nf.test

Repository: bigbio/nf-modules

Length of output: 3746

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# Check if nextflow.config.quantms sets the quantification_method parameter
cat -n ./modules/bigbio/pmultiqc/tests/nextflow.config.quantms

Repository: bigbio/nf-modules

Length of output: 427

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# Search for where this pmultiqc module is called from to see if quantification_method is set by the caller
rg 'PMULTIQC' --type=nf | grep -v test | grep -v '\.snap'

Repository: bigbio/nf-modules

Length of output: 87

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# Check if there's documentation about required parameters
find . -name 'README.md' -exec grep -l 'quantification_method' {} \;

Repository: bigbio/nf-modules

Length of output: 43

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# Look for any parent workflow configuration that might set these parameters
rg 'params\.quantification_method' -g '*.nf' -g '*.config'

Repository: bigbio/nf-modules

Length of output: 157

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# Check if the tests actually pass with the current setup
# by looking at the test snapshot results
cat -n ./modules/bigbio/pmultiqc/tests/main.nf.test.snap

Repository: bigbio/nf-modules

Length of output: 2228

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# Search the entire repository to see if quantification_method is set as a parameter anywhere
rg 'quantification_method' -C3

Repository: bigbio/nf-modules

Length of output: 1104

Add validation for required parameters and config file.

The code uses $params.quantification_method and ./results/multiqc_config.yml unconditionally without checking if they exist. This is inconsistent with how other optional parameters are handled (e.g., contaminant_affix uses a conditional expression). While tests pass because they provide these values, the code should either:

  1. Make both parameters conditional (like contaminant_affix), or
  2. Add validation to ensure they're defined before the multiqc command executes

Consider aligning with the pattern used for contaminant_affix on line 23, which checks if the parameter exists before adding it to the command.

🤖 Prompt for AI Agents 
In modules/bigbio/pmultiqc/main.nf around lines 34 to 44, the multiqc invocation
uses $params.quantification_method and ./results/multiqc_config.yml
unconditionally; update the script to either (A) conditionally append the
quantification method and config args in the command only when
params.quantification_method is defined and the config file exists (following
the same pattern used for contaminant_affix), or (B) add an explicit validation
early in the task that checks params.quantification_method is set and
./results/multiqc_config.yml exists and fail fast with a clear error message;
choose one approach and apply it consistently for both the quantification_method
and the config file.


cat <<-END_VERSIONS > versions.yml
"${task.process}":
pmultiqc: \$(multiqc --pmultiqc_version | sed -e "s/pmultiqc, version //g")
END_VERSIONS
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🌐 Web query:

pmultiqc MultiQC plugin --pmultiqc_version flag documentation

💡 Result:

I couldn't find any documented --pmultiqc_version flag in the pmultiqc or MultiQC documentation or source. The official pmultiqc docs and package pages list its command-line options but do not include that flag. See the pmultiqc GitHub and PyPI pages for the documented options. [1][2]

Would you like me to (a) search the pmultiqc source tree for an undocumented/hidden flag, (b) check a specific pmultiqc version/release, or (c) inspect your local installation (if you can paste output of multiqc --help or pip show pmultiqc)?

Sources:

  • pmultiqc GitHub repository (options & README). [1]
  • pmultiqc PyPI project page (release / usage). [2]

🌐 Web query:

multiqc --version flag and pmultiqc version reporting methods

💡 Result:

Short answer:

  • multiqc --version: prints the installed MultiQC package version and exits (e.g. "multiqc, version 1.20") — same as shown in the Quick Start/docs. [1]

  • How MultiQC reports versions in reports: MultiQC attempts to auto-detect tool versions from tool log output and shows them inline and in a "Software Versions" table. You can (a) supply manual versions in a MultiQC config under software_versions, (b) provide standalone YAML version files, or (c) disable automatic detection with disable_version_detection or hide the versions section with skip_versions_section. [2]

  • pmultiqc (the proteomics MultiQC plugin): pmultiqc is a MultiQC module/plugin — when installed it adds its own section(s) to the MultiQC report and the report's "About" area will show the MultiQC version used to generate the report. pmultiqc-specific metadata/versions are reported like other modules (from logs or via the manual software_versions YAML/config). See the pmultiqc docs/GitHub for plugin behavior and example reports. [3][2]

Sources:

  1. MultiQC Quick Start / running docs (example of multiqc --version). [1]
  2. MultiQC documentation — listing software versions, config options (software_versions, disable_version_detection, skip_versions_section). [2]
  3. pmultiqc project/docs & example reports (pmultiqc module appears in report and example reports show MultiQC version in "About"). [3]

🌐 Web query:

pmultiqc GitHub repository source code --pmultiqc_version flag implementation

💡 Result:

Do you want (A) the exact file/lines in the pmultiqc GitHub repo that implement the --pmultiqc_version flag, (B) a short explanation of how that flag is implemented, or (C) both?

🌐 Web query:

pmultiqc GitHub repository exact file and line numbers implementing --pmultiqc_version flag

💡 Result:

I can find that for you — do you mean the bigbio/pmultiqc GitHub repo (which branch or tag/version)? If so I’ll search the repository and return the exact file path(s) and line numbers that implement the --pmultiqc_version flag. Which branch/version should I use?

🏁 Script executed:

find . -type f -name "*.nf" | xargs rg -l "versions\.yml" | head -10

Repository: bigbio/nf-modules

Length of output: 171

🏁 Script executed:

cat -n ./modules/bigbio/pmultiqc/main.nf | head -60

Repository: bigbio/nf-modules

Length of output: 2055

🏁 Script executed:

cat -n ./modules/bigbio/thermorawfileparser/main.nf | grep -A 5 "versions.yml"

Repository: bigbio/nf-modules

Length of output: 691

🏁 Script executed:

cat -n ./modules/bigbio/onsite/main.nf | grep -A 5 "versions.yml"

Repository: bigbio/nf-modules

Length of output: 528

🏁 Script executed:

rg "pmultiqc_version" . --type nf

Repository: bigbio/nf-modules

Length of output: 87

🏁 Script executed:

rg "pmultiqc_version" .

Repository: bigbio/nf-modules

Length of output: 178

🌐 Web query:

how to get pmultiqc version installed pip show pmultiqc python import

💡 Result:

Ways to get the installed pmultiqc version:

  1. From pip (shell):
  • pip show pmultiqc
  • pip list | grep pmultiqc
    (works for packages installed into the active Python environment). [1]
  1. From Python by checking the package (if it exposes version):
  • python -c "import pmultiqc; print(pmultiqc.version)"
  1. From Python using importlib.metadata (recommended, works even if package has no version):
  • Python 3.8+: python -c "from importlib.metadata import version; print(version('pmultiqc'))"
  • For older Pythons, install backport and use: python -c "from importlib_metadata import version; print(version('pmultiqc'))". [2]

References:

  • pmultiqc on PyPI / project pages. [1]
  • importlib.metadata documentation (version() / distribution). [2]
  • pmultiqc GitHub / docs (install/usage). [3]

Fix the version extraction command; --pmultiqc_version is not a supported MultiQC flag.

The command multiqc --pmultiqc_version does not exist and will cause the process to fail. The standard multiqc --version outputs "multiqc, version X.X", not pmultiqc-specific versions. Use pip show pmultiqc or python -c "from importlib.metadata import version; print(version('pmultiqc'))" to extract the pmultiqc version instead.

🤖 Prompt for AI Agents 
In modules/bigbio/pmultiqc/main.nf around lines 46 to 49, the current version
extraction uses the unsupported flag `multiqc --pmultiqc_version`; replace that
with a command that queries the pmultiqc package itself (for example `pip show
pmultiqc` or `python -c "from importlib.metadata import version;
print(version('pmultiqc'))"`) and write that output into versions.yml under the
pmultiqc key; ensure you capture stderr/out properly and strip any extraneous
text so the value is just the version string.

"""
}
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