Add varnet (https://github.com/skandlab/VarNet) #11787
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| process VARNET { | ||
| tag "$meta.id" | ||
| label 'process_high_memory' | ||
|
|
||
| // Using the official VarNet Docker image | ||
| container "docker.io/kiranchari/varnet:latest" | ||
|
|
||
| input: | ||
| tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) | ||
| tuple val(meta2), path(intervals) | ||
| tuple val(meta3), path(fasta) | ||
| tuple val(meta4), path(fai) | ||
|
kiranchari marked this conversation as resolved.
Outdated
|
||
|
|
||
| output: | ||
| tuple val(meta), path("${prefix}/${prefix}.vcf.gz") , emit: vcf | ||
| tuple val("${task.process}"), val("varnet"), val("1.0.0"), emit: versions, topic: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| def regions = intervals ? "--region_bed \$WORKDIR/${intervals}" : "" | ||
| def normal = input_normal ? "--normal_bam \$WORKDIR/${input_normal}" : "" | ||
| """ | ||
|
|
||
| WORKDIR=\$(pwd) | ||
|
|
||
| cd /VarNet | ||
|
Contributor
There was a problem hiding this comment. Why are you changing the directory to here? Hence you obviously need the WORKDIR.
Author
There was a problem hiding this comment. At the moment, my scripts rely on being in the /VarNet working directory. The test input files were using relative paths based on $WORKDIR instead of absolute paths, which was causing the tests to fail. Prepending $WORKDIR was a quick fix to make those paths valid so the tests could run.
Contributor
There was a problem hiding this comment. To be honest with you, it sounds like you need to update your tool to make it functional.
Member
There was a problem hiding this comment. To elaborate a little: a key feature of Nextflow is that execution of each task is encapsulated within its work directory. That way, different tasks do not affect one another and the execution becomes much safer and more reproducible. Moving outside of the work directory violates this, and also means the pipeline is much less likely to work in diverse compute environments. eg. You typically cannot make root directories like this if you're running on a HPC using conda. |
||
| TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/filter.py \\ | ||
| --sample_name ${prefix} \\ | ||
| ${normal} \\ | ||
| --tumor_bam \$WORKDIR/${input_tumor} \\ | ||
|
Contributor
There was a problem hiding this comment. Does this really need to use WORKDIR for everything? Given it is your tool, could you patch it to respect the current working directory?
Author
There was a problem hiding this comment. I modified this because the test input files were using relative paths based on $WORKDIR instead of absolute paths, which was causing the tests to fail. Prepending $WORKDIR was a quick fix to make those paths valid so the tests could run. |
||
| --reference \$WORKDIR/${fasta} \\ | ||
| --output_dir \$WORKDIR \\ | ||
| --processes ${task.cpus} \\ | ||
| ${regions} \\ | ||
| ${args} | ||
|
|
||
| TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/predict.py \\ | ||
| --sample_name ${prefix} \\ | ||
| ${normal} \\ | ||
| --tumor_bam \$WORKDIR/${input_tumor} \\ | ||
| --reference \$WORKDIR/${fasta} \\ | ||
| --output_dir \$WORKDIR \\ | ||
| --processes ${task.cpus} \\ | ||
| ${args} | ||
|
kiranchari marked this conversation as resolved.
|
||
|
|
||
| cat <<-END_VERSIONS > \$WORKDIR/versions.yml | ||
| "${task.process}": | ||
| varnet: 1.5.0 | ||
| END_VERSIONS | ||
|
Member
There was a problem hiding this comment. please switch to topics. |
||
| """ | ||
|
|
||
| stub: | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| mkdir -p ${prefix} | ||
| echo "" | gzip > ${prefix}/${prefix}.vcf.gz | ||
|
|
||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| varnet: 1.0.0 | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| name: "varnet" | ||
| description: VarNet is a deep learning-based somatic variant caller that utilizes | ||
| a two-stage filtering and prediction architecture. It processes aligned reads from | ||
| tumor and normal data to identify somatic mutations using a deep neural network | ||
| approach. | ||
| keywords: | ||
| - variant calling | ||
| - machine learning | ||
| - neural network | ||
| - somatic | ||
| tools: | ||
| - "varnet": | ||
| description: "A deep learning-based somatic variant caller" | ||
| homepage: "https://github.com/skandlab/VarNet" | ||
| documentation: "https://github.com/skandlab/VarNet" | ||
| tool_dev_url: "https://github.com/skandlab/VarNet" | ||
| doi: "10.1038/s41467-022-31765-8" | ||
| licence: | ||
| - "PolyForm Noncommercial License 1.0.0" | ||
| identifier: "" | ||
| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - input_normal: | ||
| type: file | ||
| description: BAM/CRAM file from normal sample | ||
| pattern: "*.{bam,cram}" | ||
| ontologies: [] | ||
| - index_normal: | ||
| type: file | ||
| description: Index of normal BAM/CRAM file | ||
| pattern: "*.{bai,crai}" | ||
| ontologies: [] | ||
| - input_tumor: | ||
| type: file | ||
| description: BAM/CRAM file from tumor sample | ||
| pattern: "*.{bam,cram}" | ||
| ontologies: [] | ||
| - index_tumor: | ||
| type: file | ||
| description: Index of tumor BAM/CRAM file | ||
| pattern: "*.{bai,crai}" | ||
| ontologies: [] | ||
| - - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing reference information | ||
| - intervals: | ||
| type: file | ||
| description: BED file containing target intervals | ||
| pattern: "*.bed" | ||
| ontologies: [] | ||
| - - meta3: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing reference information | ||
| - fasta: | ||
| type: file | ||
| description: The reference fasta file | ||
| pattern: "*.{fasta,fa}" | ||
| ontologies: [] | ||
| - - meta4: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing reference information | ||
| - fai: | ||
| type: file | ||
| description: Index of reference fasta file | ||
| pattern: "*.fai" | ||
| ontologies: [] | ||
| output: | ||
| vcf: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}/${prefix}.vcf.gz: {} | ||
| vcf_tbi: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}/${prefix}.vcf.gz.tbi: {} | ||
|
Member
There was a problem hiding this comment. I feel like we're missing this in the main.nf No tbi are being emitted out |
||
| versions: | ||
| - versions.yml: {} | ||
| topics: | ||
| versions: | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - varnet: | ||
| type: string | ||
| description: The name of the tool | ||
| - 1.0.0: | ||
| type: string | ||
| description: The expression to obtain the version of the tool | ||
| authors: | ||
| - "@kiranchari" | ||
| maintainers: | ||
| - "@kiranchari" | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process VARNET" | ||
| script "../main.nf" | ||
| process "VARNET" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "varnet" | ||
|
|
||
| test("tumor_normal_pair") { | ||
| config './nextflow.config' | ||
|
SPPearce marked this conversation as resolved.
Outdated
|
||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = [ | ||
| [ id:'test_region' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) | ||
| ] | ||
| input[2] = [ | ||
| [ id:'genome' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[3] = [ | ||
| [ id:'genome' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { | ||
| assert snapshot( | ||
| process.out.vcf.collect { file(it[1]).getName() }, | ||
| process.out.vcf_tbi.collect { file(it[1]).getName() }, | ||
| process.out.versions | ||
|
kiranchari marked this conversation as resolved.
Outdated
|
||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("tumor_only") { | ||
| config './nextflow.config' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_tumor_only' ], | ||
| [], // input_normal is empty | ||
| [], // index_normal is empty | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = [ | ||
| [ id:'intervals' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) | ||
| ] | ||
| input[2] = [ | ||
| [ id:'genome' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[3] = [ | ||
| [ id:'genome' ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { | ||
| assert snapshot( | ||
| process.out.vcf.collect { file(it[1]).getName() }, | ||
| process.out.vcf_tbi.collect { file(it[1]).getName() }, | ||
| process.out.versions | ||
|
kiranchari marked this conversation as resolved.
Outdated
|
||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
| } | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| { | ||
| "tumor_only": { | ||
| "content": [ | ||
| [ | ||
| "test_tumor_only_out.vcf.gz" | ||
| ], | ||
| [ | ||
|
|
||
| ], | ||
| [ | ||
| [ | ||
| "VARNET", | ||
| "varnet", | ||
| "1.0.0" | ||
| ] | ||
| ] | ||
| ], | ||
| "timestamp": "2026-05-28T17:01:27.251285842", | ||
| "meta": { | ||
| "nf-test": "0.9.5", | ||
| "nextflow": "26.04.0" | ||
| } | ||
| }, | ||
| "tumor_normal_pair": { | ||
| "content": [ | ||
| [ | ||
| "test_out.vcf.gz" | ||
| ], | ||
| [ | ||
|
|
||
| ], | ||
| [ | ||
| [ | ||
| "VARNET", | ||
| "varnet", | ||
| "1.0.0" | ||
| ] | ||
| ] | ||
| ], | ||
| "timestamp": "2026-05-28T16:46:04.690450597", | ||
| "meta": { | ||
| "nf-test": "0.9.5", | ||
| "nextflow": "26.04.0" | ||
| } | ||
| } | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| process { | ||
| withName: VARNET { | ||
| ext.prefix = { "${meta.id}_out" } | ||
| memory = '16GB' | ||
| cpus = 1 | ||
| // ext.args is no longer needed for the region since it's handled via the input channel | ||
|
kiranchari marked this conversation as resolved.
|
||
| } | ||
| } | ||
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Is there a plan to put it on bioconda?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Not at the moment!
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Could you make one?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Note that a nf-core recommendation describes this: https://nf-co.re/docs/specifications/pipelines/recommendations/bioconda
We do make some exceptions for this but usually only for things like licensing issues etc. We have a
#biocondachannel on slack with a bunch of experts around to help :)There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
My institution requires VarNet to use a PolyForm Noncommercial License 1.0.0, which prevents adding it to bioconda. Please let me know if my understanding is incorrect.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Never heard of that one before.
From what I can tell, it allows for redistribution, which I think would mean it is compatible with bioconda. But I'm not a bioconda expert.