Added module lmm and copied kinshipmatrix module #8475
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 |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| { | ||
| "nextflow.formatting.harshilAlignment": true, | ||
| "nextflow.telemetry.enabled": false | ||
| } |
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 +1,7 @@ | ||||||
| --- | ||||||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||||||
| channels: | ||||||
| - conda-forge | ||||||
| - bioconda | ||||||
| dependencies: | ||||||
| - "bioconda::gemma=0.98.5" | ||||||
|
There was a problem hiding this comment. You don't need here the
Suggested change
|
||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,49 @@ | ||||||||||||||
| process GEMMA_KINSHIPMATRIX { | ||||||||||||||
| tag "$meta.id" | ||||||||||||||
| label 'process_single' | ||||||||||||||
|
|
||||||||||||||
| conda "${moduleDir}/environment.yml" | ||||||||||||||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||||||||||||||
| 'https://depot.galaxyproject.org/singularity/gemma:0.98.5--ha36d3ea_0': | ||||||||||||||
| 'biocontainers/gemma/0.98.5--ha36d3ea_0' }" | ||||||||||||||
|
|
||||||||||||||
| input: | ||||||||||||||
| tuple val(meta), path(genotype) | ||||||||||||||
| tuple val(meta2), path(phenotype) | ||||||||||||||
|
Comment on lines
+11
to
+12
There was a problem hiding this comment. As both files represent different information from the same dataset, they should be kept in sync and therefore in the same tuple.
Suggested change
|
||||||||||||||
|
|
||||||||||||||
| output: | ||||||||||||||
| tuple val(meta), path("output/${meta.id}.out.cXX.txt"), emit: matrix | ||||||||||||||
| path "versions.yml" , emit: versions | ||||||||||||||
|
Comment on lines
+15
to
+16
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
|
|
||||||||||||||
| when: | ||||||||||||||
| task.ext.when == null || task.ext.when | ||||||||||||||
|
|
||||||||||||||
| script: | ||||||||||||||
| def args = task.ext.args ?: '' | ||||||||||||||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||||||||||||||
|
Comment on lines
+22
to
+23
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| """ | ||||||||||||||
| gemma \\ | ||||||||||||||
| $args \\ | ||||||||||||||
| -g $genotype \\ | ||||||||||||||
| -p $phenotype \\ | ||||||||||||||
|
Comment on lines
+26
to
+28
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| -gk \\ | ||||||||||||||
|
There was a problem hiding this comment. If I'm not wrong the |
||||||||||||||
| -o ${meta.id}.out | ||||||||||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
|
|
||||||||||||||
| cat <<-END_VERSIONS > versions.yml | ||||||||||||||
| "${task.process}": | ||||||||||||||
| gemma: \$(gemma --version) | ||||||||||||||
| END_VERSIONS | ||||||||||||||
| """ | ||||||||||||||
|
|
||||||||||||||
| stub: | ||||||||||||||
| def args = task.ext.args ?: '' | ||||||||||||||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||||||||||||||
|
Comment on lines
+39
to
+40
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| """ | ||||||||||||||
| mkdir output | ||||||||||||||
| touch output/${meta.id}.out.cXX.txt | ||||||||||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| cat <<-END_VERSIONS > versions.yml | ||||||||||||||
| "${task.process}": | ||||||||||||||
| gemma: \$(gemma --version) | ||||||||||||||
| 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 +1,64 @@ | ||||||
| --- | ||||||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||||||
| name: "gemma_kinshipmatrix" | ||||||
| description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) | ||||||
| keywords: | ||||||
| - matrix | ||||||
| - lmms | ||||||
| - gwas | ||||||
|
There was a problem hiding this comment. You could add kinship here |
||||||
| tools: | ||||||
| - "gemma": | ||||||
| description: "Linear mixed models (LMMs) for genome-wide association (GWA)" | ||||||
| homepage: "https://github.com/genetics-statistics/GEMMA" | ||||||
| documentation: "https://github.com/genetics-statistics/GEMMA" | ||||||
| tool_dev_url: "https://github.com/genetics-statistics/GEMMA" | ||||||
| doi: "https://doi.org/10.1038/ng.2310" | ||||||
| licence: ["GPL v3"] | ||||||
| identifier: biotools:gemma | ||||||
|
|
||||||
| ## TODO nf-core: Add a description of all of the variables used as input | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| input: | ||||||
| - - meta: | ||||||
| type: map | ||||||
| description: | | ||||||
| Groovy Map containing sample information | ||||||
| e.g. `[ id:'sample1' ]` | ||||||
|
|
||||||
| - genotype: | ||||||
| type: file | ||||||
| description: genotype_matrix file | ||||||
|
There was a problem hiding this comment. As Gemma doesn't use a common format, could you describe briefly the columns expected ? |
||||||
| pattern: "*.txt" | ||||||
|
|
||||||
| - - meta2: | ||||||
| type: map | ||||||
| description: | | ||||||
| Groovy Map containing sample information | ||||||
| e.g. `[ id:'sample1' ]` | ||||||
|
|
||||||
| - phenotype: | ||||||
| type: file | ||||||
| description: phenotype file | ||||||
|
There was a problem hiding this comment. Same as previous comment |
||||||
| pattern: "*.txt" | ||||||
|
|
||||||
| output: | ||||||
| - heat_map: | ||||||
| - meta: | ||||||
| type: map | ||||||
| description: | | ||||||
| Groovy Map containing sample information | ||||||
| e.g. `[ id:'sample1' ]` | ||||||
| - "*.cXX.txt": | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| type: file | ||||||
| description: kinship matrix | ||||||
| pattern: "*cXX.txt" | ||||||
|
|
||||||
| - versions: | ||||||
| - "versions.yml": | ||||||
| type: file | ||||||
| description: File containing software versions | ||||||
| pattern: "versions.yml" | ||||||
|
|
||||||
| authors: | ||||||
| - "@chriswyatt1" | ||||||
| maintainers: | ||||||
| - "@chriswyatt1" | ||||||
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 +1,76 @@ | ||||||||||||||
| nextflow_process { | ||||||||||||||
|
|
||||||||||||||
| name "Test Process GEMMA_KINSHIPMATRIX" | ||||||||||||||
| script "../main.nf" | ||||||||||||||
| process "GEMMA_KINSHIPMATRIX" | ||||||||||||||
|
|
||||||||||||||
| tag "modules" | ||||||||||||||
| tag "modules_nfcore" | ||||||||||||||
| tag "gemma" | ||||||||||||||
| tag "gemma/kinshipmatrix" | ||||||||||||||
|
|
||||||||||||||
| // TODO nf-core: Change the test name preferably indicating the test-data and file-format used | ||||||||||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| test("gwas - vcf - pheno") { | ||||||||||||||
|
|
||||||||||||||
| when { | ||||||||||||||
| process { | ||||||||||||||
| """ | ||||||||||||||
| // TODO nf-core: define inputs of the process here. Example: | ||||||||||||||
|
|
||||||||||||||
|
Comment on lines
+18
to
+19
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| input[0] = [ | ||||||||||||||
| [ id:'test', single_end:false ], // meta map | ||||||||||||||
|
There was a problem hiding this comment. You do not use the
Suggested change
|
||||||||||||||
| file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.geno.txt.gz", checkIfExists: true) | ||||||||||||||
|
There was a problem hiding this comment. There is no dataset available on the nf-core/test-datasets repository ? |
||||||||||||||
|
|
||||||||||||||
| ] | ||||||||||||||
| input[1] = [ | ||||||||||||||
| [ id:'test', single_end:false ], // meta map | ||||||||||||||
|
|
||||||||||||||
| file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.pheno.txt", checkIfExists: true), | ||||||||||||||
| ] | ||||||||||||||
| """ | ||||||||||||||
| } | ||||||||||||||
| } | ||||||||||||||
|
|
||||||||||||||
| then { | ||||||||||||||
| assertAll( | ||||||||||||||
| { assert process.success }, | ||||||||||||||
| { assert snapshot(process.out).match() } | ||||||||||||||
| ) | ||||||||||||||
| } | ||||||||||||||
|
|
||||||||||||||
| } | ||||||||||||||
|
|
||||||||||||||
| // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. | ||||||||||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||||||||||
| test("gwas - vcf - pheno - stub") { | ||||||||||||||
|
|
||||||||||||||
| options "-stub" | ||||||||||||||
|
|
||||||||||||||
| when { | ||||||||||||||
| process { | ||||||||||||||
| """ | ||||||||||||||
| // TODO nf-core: define inputs of the process here. Example: | ||||||||||||||
|
|
||||||||||||||
|
||||||||||||||
| // TODO nf-core: define inputs of the process here. Example: |
Comment on lines
+69
to
+70
There was a problem hiding this comment.
Suggested change
| { assert snapshot(process.out).match() } | |
| //TODO nf-core: Add all required assertions to verify the test output. | |
| { assert snapshot( | |
| process.out, | |
| path(process.out.versions[0]).yaml | |
| ).match() } |
|
There was a problem hiding this comment. Could you delete and regenerate the snapshot file ? |
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 +1,128 @@ | ||
| { | ||
| "sarscov2 - bam - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| [ | ||
|
|
||
|
There was a problem hiding this comment. Could you update the test such as a empty file is correctly generated here ? |
||
| ] | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,02383d9d5046a267d81f99463df55749" | ||
| ], | ||
| "matrix": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| [ | ||
|
|
||
| ] | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,02383d9d5046a267d81f99463df55749" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "25.04.2" | ||
| }, | ||
| "timestamp": "2025-05-14T16:34:56.015094848" | ||
| }, | ||
| "gwas - vcf - pheno - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
|
|
||
| ], | ||
| "1": [ | ||
|
|
||
| ], | ||
| "matrix": [ | ||
|
|
||
| ], | ||
| "versions": [ | ||
|
|
||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "25.04.2" | ||
| }, | ||
| "timestamp": "2025-05-14T17:51:24.26939259" | ||
| }, | ||
| "sarscov2 - bam": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| [ | ||
| "test.out.cXX.txt:md5,83fbef03ff6c4e7e89bebd52ce9d11a6", | ||
| "test.out.log.txt:md5,f7eccba3f5e053669b3fb2b8c5f635e7" | ||
| ] | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,02383d9d5046a267d81f99463df55749" | ||
| ], | ||
| "matrix": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| [ | ||
| "test.out.cXX.txt:md5,83fbef03ff6c4e7e89bebd52ce9d11a6", | ||
| "test.out.log.txt:md5,f7eccba3f5e053669b3fb2b8c5f635e7" | ||
| ] | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,02383d9d5046a267d81f99463df55749" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "25.04.2" | ||
| }, | ||
| "timestamp": "2025-05-14T16:34:38.506668318" | ||
| }, | ||
| "gwas - vcf - pheno": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
|
|
||
| ], | ||
| "1": [ | ||
|
|
||
| ], | ||
| "matrix": [ | ||
|
|
||
| ], | ||
| "versions": [ | ||
|
|
||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "25.04.2" | ||
| }, | ||
| "timestamp": "2025-05-14T17:51:16.641698027" | ||
| } | ||
| } | ||
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 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::gemma=0.98.5" |
|
There was a problem hiding this comment. Could you update this file similarly as the kinshipmatrix process ? |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||||
|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,54 @@ | ||||||||
| process GEMMA_LMM { | ||||||||
| tag "$meta.id" | ||||||||
| label 'process_single' | ||||||||
|
|
||||||||
| conda "${moduleDir}/environment.yml" | ||||||||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||||||||
| 'https://depot.galaxyproject.org/singularity/gemma:0.98.5--ha36d3ea_0': | ||||||||
| 'community.wave.seqera.io/library/gemma:0.98.5--87bf3eea4b1ea0ad' }" | ||||||||
|
|
||||||||
| input: | ||||||||
| tuple val(meta), path(genotype) | ||||||||
| tuple val(meta2), path(phenotype) | ||||||||
|
Comment on lines
+11
to
+12
There was a problem hiding this comment.
Suggested change
|
||||||||
| tuple val(meta3), path(annot) | ||||||||
| tuple val(meta4), path(cXX) | ||||||||
|
|
||||||||
| output: | ||||||||
| tuple val(meta), path("output/${meta.id}.out.assoc.txt"), emit: matrix | ||||||||
| path "versions.yml" , emit: versions | ||||||||
|
|
||||||||
| when: | ||||||||
| task.ext.when == null || task.ext.when | ||||||||
|
|
||||||||
| script: | ||||||||
| def args = task.ext.args ?: '' | ||||||||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||||||||
| """ | ||||||||
| gemma \\ | ||||||||
| $args \\ | ||||||||
| -g $genotype \\ | ||||||||
| -p $phenotype \\ | ||||||||
| -n 4 \\ | ||||||||
|
There was a problem hiding this comment. Why is it hard coded here ? |
||||||||
| -a $annot \\ | ||||||||
| -k $cXX \\ | ||||||||
| -lmm \\ | ||||||||
| -o ${meta.id}.out | ||||||||
|
|
||||||||
| cat <<-END_VERSIONS > versions.yml | ||||||||
| "${task.process}": | ||||||||
| gemma: \$(gemma --version) | ||||||||
| END_VERSIONS | ||||||||
| """ | ||||||||
|
|
||||||||
| stub: | ||||||||
| def args = task.ext.args ?: '' | ||||||||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||||||||
| """ | ||||||||
| mkdir output | ||||||||
| touch output/${meta.id}.out.assoc.txt | ||||||||
| cat <<-END_VERSIONS > versions.yml | ||||||||
| "${task.process}": | ||||||||
| gemma: \$(gemma --version) | ||||||||
| END_VERSIONS | ||||||||
| """ | ||||||||
| } | ||||||||
Oops, something went wrong.
Oops, something went wrong.
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.
Could you fall back this change ?