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Added agat/spfilterfeaturefromkilllist (#5771)
* Added agat/spfilterfeaturefromkilllist * Added AGAT config * Included test with agat config
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modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| name: "agat_spfilterfeaturefromkilllist" | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - "bioconda::agat=1.4.0" |
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| process AGAT_SPFILTERFEATUREFROMKILLLIST { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
|
|
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| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/agat:1.4.0--pl5321hdfd78af_0': | ||
| 'biocontainers/agat:1.4.0--pl5321hdfd78af_0' }" | ||
|
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| input: | ||
| tuple val(meta), path(gff) | ||
| path kill_list | ||
| path config | ||
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| output: | ||
| tuple val(meta), path("*.gff"), emit: gff | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def config_param = config ? "--config $config" : '' | ||
| if( "$gff" == "${prefix}.gff" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| agat_sp_filter_feature_from_kill_list.pl \\ | ||
| --gff $gff \\ | ||
| --kill_list $kill_list \\ | ||
| $config_param \\ | ||
| $args \\ | ||
| --output "${prefix}.gff" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_filter_feature_from_kill_list.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
|
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| if( "$gff" == "${prefix}.gff" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| touch "${prefix}.gff" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_filter_feature_from_kill_list.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "agat_spfilterfeaturefromkilllist" | ||
| description: | | ||
| The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. | ||
| If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 | ||
| or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will | ||
| automatically remove this feature too. | ||
| keywords: | ||
| - genomics | ||
| - gff | ||
| - remove | ||
| - feature | ||
| tools: | ||
| - "agat": | ||
| description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." | ||
| homepage: "https://agat.readthedocs.io/en/latest/" | ||
| documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html" | ||
| tool_dev_url: "https://github.com/NBISweden/AGAT" | ||
| doi: "10.5281/zenodo.3552717" | ||
| licence: ["GPL v3"] | ||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - gff: | ||
| type: file | ||
| description: Input GFF3 file that will be read | ||
| pattern: "*.{gff,gff3}" | ||
| - kill_list: | ||
| type: file | ||
| description: Kill list. One value per line. | ||
| pattern: "*.txt" | ||
| - config: | ||
| type: file | ||
| description: | | ||
| Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). | ||
| pattern: "*.yaml" | ||
|
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||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ] | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - gff: | ||
| type: file | ||
| description: Output GFF file. | ||
| pattern: "*.gff" | ||
|
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||
| authors: | ||
| - "@GallVp" | ||
| maintainers: | ||
| - "@GallVp" |
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104
modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test
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| nextflow_process { | ||
|
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| name "Test Process AGAT_SPFILTERFEATUREFROMKILLLIST" | ||
| script "../main.nf" | ||
| process "AGAT_SPFILTERFEATUREFROMKILLLIST" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "agat" | ||
| tag "agat/spfilterfeaturefromkilllist" | ||
|
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| test("sarscov2 - gff3") { | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) | ||
| ] | ||
| def kill_list = "unknown_transcript_1" | ||
| def kill_list_file = new File('kill.list.txt') | ||
| kill_list_file.text = kill_list | ||
| input[1] = kill_list_file.toPath() | ||
| input[2] = [] | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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| } | ||
|
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| test("sarscov2 - gff3 - config") { | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) | ||
| ] | ||
| def kill_list = "unknown_transcript_1" | ||
| def kill_list_file = new File('kill.list.txt') | ||
| kill_list_file.text = kill_list | ||
| input[1] = kill_list_file.toPath() | ||
| input[2] = file(params.modules_testdata_base_path + 'generic/config/agat_config.yaml', checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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| } | ||
|
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| test("sarscov2 - gff3 - stub") { | ||
|
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| options "-stub" | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) | ||
| ] | ||
| def kill_list = "unknown_transcript_1" | ||
| def kill_list_file = new File('kill.list.txt') | ||
| kill_list_file.text = kill_list | ||
| input[1] = kill_list_file.toPath() | ||
| input[2] = [] | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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||
| } | ||
|
|
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| } |
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101
modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| { | ||
| "sarscov2 - gff3 - config": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,df19e1b84ba6f691d20c72b397c88abf" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,df19e1b84ba6f691d20c72b397c88abf" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-07-03T15:32:54.707393" | ||
| }, | ||
| "sarscov2 - gff3 - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-07-03T15:32:59.888053" | ||
| }, | ||
| "sarscov2 - gff3": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,df19e1b84ba6f691d20c72b397c88abf" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,df19e1b84ba6f691d20c72b397c88abf" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2962240799182aee69421c746be183a" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-07-03T15:32:47.772624" | ||
| } | ||
| } |
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