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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::agat=1.4.2" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| process AGAT_CONVERTBED2GFF { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/agat:1.4.2--pl5321hdfd78af_0' : | ||
| 'biocontainers/agat:1.4.2--pl5321hdfd78af_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(bed) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.gff") , emit: gff | ||
| 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}" | ||
| """ | ||
| agat_convert_bed2gff.pl \\ | ||
| --bed $bed \\ | ||
| --output ${prefix}.gff \\ | ||
| $args | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.gff | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: agat_convertbed2gff | ||
| description: | | ||
| Takes a bed12 file and converts to a GFF3 file | ||
| keywords: | ||
| - genome | ||
| - bed | ||
| - gff | ||
| - conversion | ||
| tools: | ||
| - agat: | ||
| description: "AGAT is a toolkit for manipulation and getting information from | ||
| GFF/GTF files" | ||
| homepage: "https://github.com/NBISweden/AGAT" | ||
| documentation: "https://agat.readthedocs.io/" | ||
| tool_dev_url: "https://github.com/NBISweden/AGAT" | ||
| doi: "10.5281/zenodo.3552717" | ||
| licence: ["GPL v3"] | ||
| identifier: biotools:AGAT | ||
| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - bed: | ||
| type: file | ||
| description: Input bed12 file | ||
| pattern: "*.bed" | ||
| output: | ||
| - gff: | ||
| - meta: | ||
| type: map | ||
| description: Groovy Map containing sample information | ||
| - "*.gff": | ||
| type: file | ||
| description: Output GFF3 file | ||
| pattern: "*.{gff}" | ||
| - versions: | ||
| - versions.yml: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
|
|
||
| authors: | ||
| - "@GallVp" | ||
| maintainers: | ||
| - "@GallVp" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process AGAT_CONVERTBED2GFF" | ||
| script "../main.nf" | ||
| process "AGAT_CONVERTBED2GFF" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "agat" | ||
| tag "agat/convertbed2gff" | ||
|
|
||
| test("sarscov2 - bed12") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("sarscov2 - bam - stub") { | ||
|
|
||
| options "-stub" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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modules/nf-core/agat/convertbed2gff/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| { | ||
| "sarscov2 - bam - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-15T14:02:09.48826" | ||
| }, | ||
| "sarscov2 - bed12": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-15T14:02:03.549345" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::agat=1.4.0 | ||
| - bioconda::agat=1.4.2 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::agat=1.4.0 | ||
| - bioconda::agat=1.4.2 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::agat=1.4.0 | ||
| - bioconda::agat=1.4.2 | ||
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