new process: picard/samtofastq

[kelly-sovacool]

Add a new process PICARD_SAMTOFASTQ. Resolves #4176.

I started creating this module when pytest was used for testing, and I haven't been able to get nf-test working in my dev environment. If someone could take over generating tests for this PR that would be appreciated!

If it's helpful, here is the test main.nf file I initially created for use with pytest: https://github.com/nf-core/modules/blob/119444e25af2544ffc43da16b8c47e92cd7dfb00/tests/modules/nf-core/picard/samtofastq/main.nf

PR checklist

Closes ##4176

• 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 module conventions in the contribution docs
• [ ] If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile conda

[Copilot]

Pull request overview

Adds a new nf-core module process PICARD_SAMTOFASTQ under modules/nf-core/picard/samtofastq to convert SAM/BAM inputs into FASTQ output.

Changes:

• Introduces the PICARD_SAMTOFASTQ process implementation (conda/container, inputs/outputs, stub).
• Adds module metadata (meta.yml) describing inputs/outputs and tool information.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 11 comments.

File	Description
modules/nf-core/picard/samtofastq/main.nf	New Nextflow process definition for running Picard SamToFastq and emitting reads + version info.
modules/nf-core/picard/samtofastq/meta.yml	New module metadata describing the process interface and Picard tool details.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

The bam input in the metadata lacks a pattern (and ontologies) field, unlike other modules in this repo (including other Picard modules). Adding a pattern such as *.{bam,sam} makes the interface clearer and helps with automated validation/linting.

Suggested change

	SAM or BAM file
	SAM or BAM file
	pattern: "*.{bam,sam}"
	ontologies: ["EDAM:format_2572", "EDAM:format_2573"]

[Copilot]

tag "$meta.id" does not interpolate meta.id in Groovy (only $meta would). Use ${meta.id} so the tag shows the sample id instead of the literal .id suffix in logs.

Suggested change

	tag "$meta.id"
	tag "${meta.id}"

[Copilot]

Other modules/nf-core/picard/* modules standardize on conda "${moduleDir}/environment.yml" plus the Wave container URL for Picard (e.g. bedtointervallist/main.nf). This module hard-codes a conda package string and a different container source/version; consider aligning with the established Picard module pattern to keep dependency management consistent.

Suggested change

	conda "bioconda::picard=3.1.0"
	container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
	'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
	'biocontainers/picard:3.1.0--hdfd78af_0' }"
	conda "${moduleDir}/environment.yml"
	container "https://wave.seqera.io/library/biocontainers/picard:3.1.0--hdfd78af_0"

[Copilot]

The Picard documentation: URL points to the FastqToSam page, not SamToFastq. Update it to the correct SamToFastq documentation to avoid misleading module users.

Suggested change

	documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-
	documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-SamToFastq-Picard-

[Copilot]

The metadata is missing the identifier: biotools:picard_tools field that other Picard modules include under tools.picard (e.g. picard/fastqtosam/meta.yml). Adding it keeps tool metadata consistent across the Picard module set.

[Copilot]

The process declares path("*.fastq") as output, but the script writes ${prefix}.fastq.gz (and _1/_2.fastq.gz for paired-end). This mismatch will cause Nextflow to not capture outputs; update the output glob to match the actual filenames/extensions.

[Copilot]

The stub uses touch ${output}, but output contains Picard CLI flags (e.g. --FASTQ file ... --SECOND_END_FASTQ file ...). This will fail (touch sees --FASTQ as an option) and it won’t create the expected output files for stub runs; touch only the actual fastq filenames instead.

[Copilot]

This module introduces new behavior but doesn’t include an nf-test test suite (compare to other Picard modules such as modules/nf-core/picard/cleansam/tests). Adding at least a basic test for single-end and paired-end output naming would prevent regressions.

[Copilot]

The versions_picard metadata command is for BedToIntervalList, but this module runs SamToFastq. This should be updated so the recorded version command matches the actual tool invocation.

Suggested change

	- "picard BedToIntervalList --version 2>&1 | sed -n 's/.*Version://p'":
	- "picard SamToFastq --version 2>&1 | sed -n 's/.*Version://p'":

[Copilot]

The reads output is described as a single fastq file with pattern *.{fastq}, but the process produces gzipped FASTQ(s) (*.fastq.gz, potentially _1/_2). Align the metadata with nf-core conventions by using globbed output keys (e.g. "*.fastq.gz") and an appropriate pattern that covers single- and paired-end outputs.

Suggested change

	pattern: "*.{fastq}"
	pattern: "*.fastq.gz"