canvas_germline

[ktruve]

The tool is Illumina Canvas, a copy number variant (CNV) caller for whole genome sequencing data.
https://github.com/Illumina/canvas

There is no conda/bioconda package available for v1.40.0. The existing Bioconda recipe covers v1.35, which uses Mono as runtime. Version 1.40.0 switched to .NET Core 2.0, which is not
available on conda-forge. A custom Docker image is therefore used:
ghcr.io/clinicalgenomicsgbg/canvas:1.40.0

PR checklist

Closes #XXX

• [ X] This comment contains a description of changes (with reason).
• [ X] 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
• [X ] If necessary, include test data in your PR.
• [ X] Remove all TODO statements.
• [X ] Broadcast software version numbers to topic: versions - See version_topics
• [ X] Follow the naming conventions.
• [ X] Follow the parameters requirements.
• [ X] Follow the input/output options guidelines.
• [ X] Add a resource label
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • [ X] nf-core modules test <MODULE> --profile singularity

[famosab]

Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join.

[famosab]

I started with giving some hints that hopefully help to finalize this module a bit more :) I think the module specifications can also help quite a bit to finalize this or looking at other modules might help.

[ktruve]

Hi! I've pushed updated tests reflecting the refactored input structure (sex and ploidy VCFs combined into a tuple). I'm currently waiting for CI to run. Regarding the container: I don't yet have access to the nf-core Slack #request-core channel (still waiting for org membership). Could you help with uploading the image to quay.io/biocontainers ? The image is public at ghcr.io/clinicalgenomicsgbg/canvas:1.40.0.

[famosab]

Did you do that:

Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join.

YOu can also find the request core channel in that slack

[mashehu]

Is there no chance to add this tool to bioconda?

[ktruve]

Hi, Canvas v1.40.0 is not available on Bioconda. The existing Bioconda recipe covers v1.35, which uses Mono as runtime. Version 1.40.0 switched to .NET Core 2.0, which is not available on conda-forge and has not been packaged for newer .NET runtimes. Since the tool is archived (no active development since 2021), a new Bioconda recipe is unlikely to be maintained. I have a custom Docker image at ghcr.io/clinicalgenomicsgbg/canvas:1.40.0 (public) Would be great if it could be uploaded to quay.io/biocontainers? Best, Katarina On 13 Apr 2026, at 15:24, Matthias Hörtenhuber ***@***.***> wrote: [https://avatars.githubusercontent.com/u/6169021?s=20&v=4]mashehu left a comment (nf-core/modules#11164)<#11164 (comment)> Is there no chance to add this tool to bioconda? — Reply to this email directly, view it on GitHub<#11164 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5JMZXTBQUBGMP4CQDF7R4D4VTTAXAVCNFSM6AAAAACXXBC7AKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DEMZWG4YDMNBYGY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[mashehu]

container is now pushed to quay.io https://quay.io/repository/nf-core/canvas?tab=tags

[famosab]

Can you merge the master branch into yours? (click update branch)

[famosab]

Can you go through the review comments (also the ones that were already made prior) and either resolve them or click resolve if its something that has already been addressed?

I think the main thing is adding real tests (not only stub).

[ktruve]

Hi, Thank you for the review. I will go through all previous comments and resolve them. Regarding real tests: Canvas requires whole-genome sequencing data to run — it needs sufficient genome-wide coverage to call CNVs. It is not possible to run it on the small test datasets available in nf-core/test-datasets (chromosome-level, ~50 MB limit). Stub-only tests are therefore the only viable option for this module, similar to other modules that wrap tools with large data requirements. Best, Katarina On 15 Apr 2026, at 12:17, Famke Bäuerle ***@***.***> wrote: @famosab commented on this pull request. Can you go through the review comments (also the ones that were already made prior) and either resolve them or click resolve if its something that has already been addressed? I think the main thing is adding real tests (not only stub).

________________________________ On modules/nf-core/canvas/germline/tests/main.nf.test<#11164 (comment)>: Can we have non-stub tests?

________________________________ In modules/nf-core/canvas/germline/tests/main.nf.test.snap<#11164 (comment)>:

@@ -0,0 +1,116 @@

+{ + "homo_sapiens - bam - female - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "/clinical/dev/cgg-rd/modules/.nf-test/tests/820adc46fa7e25ac19d769b80cca2e54/work/8c/d300ac181db82932d1f0bda74cb00e/test.vcf.gz" I think something is off this should not be a path like this.

________________________________ In modules/nf-core/canvas/germline/tests/main.nf.test<#11164 (comment)>:

+ input[2] = [

+ "female", + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ⬇️ Suggested change - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(prcess.out)).match() }

________________________________ In modules/nf-core/canvas/germline/tests/main.nf.test<#11164 (comment)>:

+ input[2] = [

+ "male", + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ⬇️ Suggested change - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() }

________________________________ In modules/nf-core/canvas/germline/main.nf<#11164 (comment)>:

+ label 'process_high'

+ + container "quay.io/nf-core/canvas:1.40.0" + + input: + tuple val(meta), path(bam), path(bai) + path germline_snv_vcf + tuple val(sex), path(male_ploidy_vcf), path(female_ploidy_vcf) + path genomedir + path reference + path filter13 + + output: + tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf + tuple val(meta), path("${prefix}.CoverageAndVariantFrequency.txt"), emit: covandvarfreq + tuple val("${task.process}"), val('canvas'), val('1.40.0.1613+master'), topic: versions, emit: versions_canvas ⬇️ Suggested change - tuple val("${task.process}"), val('canvas'), val('1.40.0.1613+master'), topic: versions, emit: versions_canvas + tuple val("${task.process}"), val('canvas'), val('1.40.0'), topic: versions, emit: versions_canvas + // --version not supported by CLI, please update this manually when updating the tool — Reply to this email directly, view it on GitHub<#11164 (review)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5JMZXT6Q37ZPMFIDOSM4XD4V5OVNAVCNFSM6AAAAACXXBC7AKVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHM2DCMJSGY3TKNZUGQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>