From 0c38de27014f9a7476f6784df30bd21f618b8b95 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 28 Jan 2026 14:45:00 +0100
Subject: [PATCH] Add tools arguments ADR [ci skip]

Introduces specification for typed tool arguments in module definitions:
- Extend tools section in meta.yaml with args component
- Argument attributes: type, enum, prefix, default, description
- Script usage via tools implicit variable
- Configuration and CLI override mechanisms
- Migration guide from ext.args pattern

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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+# Tools Arguments
+
+- Authors: Paolo Di Tommaso
+- Status: draft
+- Date: 2026-01-28
+- Tags: modules, tools, arguments, configuration
+
+## Context and Problem Statement
+
+The current adoption of `task.ext.args` for passing tool arguments in Nextflow modules is extremely convoluted. This pattern makes it impossible to have a consistent, programmatic definition for parameters exposed by a module.
+
+**Current approach (problematic):**
+```groovy
+process BWA_MEM {
+    script:
+    def args = task.ext.args ?: ''
+    """
+    bwa mem $args -t $task.cpus $index $reads
+    """
+}
+```
+
+```groovy
+// Configuration
+withName: 'BWA_MEM' {
+    ext.args = '-K 100000000 -Y'
+}
+```
+
+**Problems:**
+- Arguments are opaque strings with no validation
+- No documentation of available options
+- No type safety or IDE support
+- Easy to introduce typos or invalid combinations
+- Impossible to programmatically introspect module capabilities
+
+## Decision
+
+Extend the `tools` definition in the module spec (`meta.yaml`) to support an `args` component that declares exposed tool command line arguments.
+
+**Key requirement:** The argument name must match the tool's actual option name.
+
+## Tool Arguments Specification
+
+### Definition in meta.yaml
+
+```yaml
+tools:
+  - samtools:
+      description: SAMtools
+      homepage: http://www.htslib.org/
+      args:
+        output_fmt:
+          type: string
+          enum: ["sam", "bam", "cram"]
+          description: "Output format"
+
+  - bwa:
+      description: BWA aligner
+      homepage: http://bio-bwa.sourceforge.net/
+      args:
+        K:
+          type: integer
+          description: "Process INT input bases in each batch"
+          prefix: '-'
+        Y:
+          type: boolean
+          description: "Use soft clipping for supplementary alignments"
+          prefix: '-'
+```
+
+### Argument Attributes
+
+| Attribute | Required | Default | Description |
+|-----------|----------|---------|-------------|
+| `type` | No | `string` | Data type: `boolean`, `integer`, `float`, `string` |
+| `description` | No | - | Human-readable description |
+| `enum` | No | - | List of allowed values |
+| `prefix` | No | `'--'` | Command-line prefix for the argument |
+| `default` | No | - | Default value if not configured |
+
+### Prefix Resolution
+
+The argument prefix determines how the argument is formatted on the command line:
+
+| Argument | Prefix | Value | Resolved |
+|----------|--------|-------|----------|
+| `output_fmt` | `--` (default) | `"cram"` | `--output_fmt cram` |
+| `K` | `-` | `100000000` | `-K 100000000` |
+| `Y` | `-` | `true` | `-Y` |
+
+**Boolean arguments:** When `type: boolean` and value is `true`, only the prefix+name is emitted (no value).
+
+## Script Usage
+
+In module scripts, access arguments via the `tools` implicit variable:
+
+```groovy
+process BWA_MEM {
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: aligned
+
+    script:
+    // tools.bwa.args.K → "-K 100000000"
+    // tools.bwa.args.Y → "-Y"
+    // tools.bwa.args   → "-K 100000000 -Y"  (all args concatenated)
+    """
+    bwa mem ${tools.bwa.args} -t $task.cpus $index $reads \
+        | samtools sort ${tools.samtools.args} -o ${prefix}.bam -
+    """
+}
+```
+
+### Implicit Variable Reference
+
+| Expression | Description | Example Output |
+|------------|-------------|----------------|
+| `tools.<tool>.args.<arg>` | Single formatted argument | `"-K 100000000"` |
+| `tools.<tool>.args` | All arguments concatenated | `"-K 100000000 -Y"` |
+
+## Configuration Usage
+
+Arguments are configured using `tools.<toolname>.args.<argname>`:
+
+```groovy
+process {
+    withName: 'BWA_MEM' {
+        tools.bwa.args.K = 100000000
+        tools.bwa.args.Y = true
+        tools.samtools.args.output_fmt = "cram"
+    }
+}
+```
+
+## CLI Usage
+
+Arguments can be overridden via CLI:
+
+```bash
+# For module run command
+nextflow module run nf-core/bwa-align \
+    --tools.bwa.K=100000000 \
+    --tools.bwa.Y \
+    --tools.samtools.output_fmt=cram
+
+# For standard workflow execution
+nextflow run <script> \
+    -process.BWA_MEM.tools.bwa.K=100000000 \
+    -process.BWA_MEM.tools.bwa.Y \
+    -process.BWA_MEM.tools.samtools.output_fmt=cram
+```
+
+## Benefits
+
+| Aspect | `ext.args` (Legacy) | Tool Arguments (New) |
+|--------|---------------------|----------------------|
+| Documentation | None | In meta.yaml |
+| Type Safety | None | Validated |
+| IDE Support | None | Autocompletion |
+| Introspection | Impossible | Programmatic access |
+| Validation | None | Type + enum validation |
+| Clarity | Opaque strings | Named, typed arguments |
+
+## Complete Example
+
+### meta.yaml
+
+```yaml
+name: nf-core/bwa-align
+version: "1.2.4"
+description: Align reads to reference genome using BWA-MEM algorithm
+
+requires:
+  nextflow: ">=24.04.0"
+
+tools:
+  - bwa:
+      description: |
+        BWA is a software package for mapping DNA sequences
+        against a large reference genome.
+      homepage: http://bio-bwa.sourceforge.net/
+      documentation: https://bio-bwa.sourceforge.net/bwa.shtml
+      doi: 10.1093/bioinformatics/btp324
+      license: ["GPL-3.0-or-later"]
+      identifier: biotools:bwa
+      args:
+        K:
+          type: integer
+          description: "Process INT input bases in each batch"
+          prefix: '-'
+        Y:
+          type: boolean
+          description: "Use soft clipping for supplementary alignments"
+          prefix: '-'
+        T:
+          type: integer
+          description: "Minimum score to output"
+          prefix: '-'
+          default: 30
+
+  - samtools:
+      description: Tools for manipulating alignments in SAM/BAM format
+      homepage: http://www.htslib.org/
+      license: ["MIT"]
+      identifier: biotools:samtools
+      args:
+        output_fmt:
+          type: string
+          enum: ["sam", "bam", "cram"]
+          description: "Output format"
+          default: "bam"
+        threads:
+          type: integer
+          description: "Number of threads"
+          prefix: '-@'
+```
+
+### main.nf
+
+```groovy
+process BWA_MEM {
+    input:
+    tuple val(meta), path(reads)
+    tuple val(meta2), path(index)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: aligned
+    path "versions.yml", emit: versions
+
+    script:
+    def prefix = meta.id
+    """
+    bwa mem ${tools.bwa.args} -t $task.cpus $index $reads \
+        | samtools sort ${tools.samtools.args} -o ${prefix}.bam -
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwa: \$(bwa 2>&1 | grep Version | cut -d' ' -f2)
+        samtools: \$(samtools --version | head -1 | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
+```
+
+### Configuration
+
+```groovy
+process {
+    withName: 'BWA_MEM' {
+        tools.bwa.args.K = 100000000
+        tools.bwa.args.Y = true
+        tools.samtools.args.output_fmt = "cram"
+    }
+}
+```
+
+## Migration from ext.args
+
+### Before (Legacy)
+
+```groovy
+// main.nf
+process BWA_MEM {
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    """
+    bwa mem $args -t $task.cpus $index $reads | samtools sort $args2 -o out.bam -
+    """
+}
+
+// nextflow.config
+withName: 'BWA_MEM' {
+    ext.args = '-K 100000000 -Y'
+    ext.args2 = '--output-fmt cram'
+}
+```
+
+### After (Tool Arguments)
+
+```groovy
+// main.nf
+process BWA_MEM {
+    script:
+    """
+    bwa mem ${tools.bwa.args} -t $task.cpus $index $reads \
+        | samtools sort ${tools.samtools.args} -o out.bam -
+    """
+}
+
+// nextflow.config
+withName: 'BWA_MEM' {
+    tools.bwa.args.K = 100000000
+    tools.bwa.args.Y = true
+    tools.samtools.args.output_fmt = "cram"
+}
+```
+
+## Rationale
+
+**Why argument names must match tool options?**
+- Eliminates mapping layer between config and actual tool
+- Users familiar with the tool can immediately understand the config
+- Documentation can link directly to tool manuals
+- Reduces cognitive overhead and potential for errors
+
+**Why per-tool namespacing?**
+- Modules often wrap multiple tools (e.g., bwa + samtools)
+- Clear separation prevents argument name collisions
+- Enables tool-specific documentation and validation
+
+**Why typed arguments?**
+- Catch errors at configuration time, not runtime
+- Enable IDE autocompletion and validation
+- Support for enums provides constrained choices
+
+## Open Questions
+
+1. **Argument ordering**: Should the order of `tools.<tool>.args` output match declaration order in meta.yaml or be alphabetical?
+
+2. **Conditional arguments**: How to handle arguments that are mutually exclusive or have dependencies?
+
+3. **Complex argument formats**: How to handle arguments with complex formats like `-I file1 -I file2` (repeated flags)?
+
+## Open Problems
+
+### Subcommand argument collision
+
+A tool having the same option name in two different subcommands cannot be managed with the current design. Arguments are defined at the tool level, not at the subcommand level.
+
+**Example:** `samtools view` and `samtools sort` both have a `-o` option with different semantics:
+
+```bash
+samtools view -o output.bam input.bam    # output file for view
+samtools sort -o output.bam input.bam    # output file for sort
+```
+
+With the current spec, there's no way to distinguish between these:
+
+```yaml
+tools:
+  - samtools:
+      args:
+        o:
+          type: string
+          prefix: '-'
+          description: "Output file"  # Which subcommand?
+```
+
+**Potential solutions (not addressed in this ADR):**
+- Subcommand namespacing: `tools.samtools.view.args.o` vs `tools.samtools.sort.args.o`
+- Argument aliasing: Define tool-level unique names that map to subcommand options
+- Scope limitation: Only support arguments that are consistent across subcommands