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Merge pull request #26 from GallVp/repeatmasker/rmOutToGFF3
Added repeatmasker/rmouttogff3
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| name: "repeatmasker_rmouttogff3" | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - "bioconda::repeatmasker=4.1.5" |
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| process REPEATMASKER_RMOUTTOGFF3 { | ||
| tag "$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/repeatmasker:4.1.5--pl5321hdfd78af_0': | ||
| 'biocontainers/repeatmasker:4.1.5--pl5321hdfd78af_0' }" | ||
|
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| input: | ||
| tuple val(meta), path(out) | ||
|
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| output: | ||
| tuple val(meta), path("*.gff3") , emit: gff3 | ||
| 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}" | ||
|
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| """ | ||
| rm_path=\$(dirname \$(realpath \$(which RepeatMasker))) | ||
| PERL5LIB=\$rm_path rmOutToGFF3.pl \\ | ||
| $out \\ | ||
| > ${prefix}.gff3 | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') | ||
| END_VERSIONS | ||
| """ | ||
|
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.gff3 | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,51 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "repeatmasker_rmouttogff3" | ||
| description: A utility script to assist to convert old RepeatMasker *.out files to version 3 gff files. | ||
| keywords: | ||
| - sort | ||
| - example | ||
| - genomics | ||
| tools: | ||
| - repeatmasker: | ||
| description: | | ||
| RepeatMasker is a program that screens DNA sequences for interspersed | ||
| repeats and low complexity DNA sequences | ||
| homepage: "https://www.repeatmasker.org/" | ||
| documentation: "https://www.repeatmasker.org/webrepeatmaskerhelp.html" | ||
| tool_dev_url: "https://github.com/rmhubley/RepeatMasker" | ||
| licence: ["Open Software License v. 2.1"] | ||
|
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||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ]` | ||
| - out: | ||
| type: file | ||
| description: RepeatMasker out file | ||
| pattern: "*.out" | ||
|
|
||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ]` | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
|
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||
| - gff3: | ||
| type: file | ||
| description: Sorted BAM/CRAM/SAM file | ||
| pattern: "*.gff3" | ||
|
|
||
| authors: | ||
| - "@GallVp" | ||
| maintainers: | ||
| - "@GallVp" |
68 changes: 68 additions & 0 deletions
68
modules/gallvp/repeatmasker/rmouttogff3/tests/main.nf.test
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|---|---|---|
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| nextflow_process { | ||
|
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| name "Test Process REPEATMASKER_RMOUTTOGFF3" | ||
| script "../main.nf" | ||
| process "REPEATMASKER_RMOUTTOGFF3" | ||
|
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| tag "modules" | ||
| tag "modules_gallvp" | ||
| tag "repeatmasker" | ||
| tag "repeatmasker/rmouttogff3" | ||
| tag "repeatmasker/repeatmasker" | ||
|
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| setup { | ||
| run("REPEATMASKER_REPEATMASKER") { | ||
| script "../../repeatmasker" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
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| test("sarscov2 - genome - fasta - repeatmasker - out") { | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = REPEATMASKER_REPEATMASKER.out.out | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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| } | ||
|
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| test("sarscov2 - genome - fasta - repeatmasker - out - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = input[0] = REPEATMASKER_REPEATMASKER.out.out | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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| } | ||
|
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||
| } |
72 changes: 72 additions & 0 deletions
72
modules/gallvp/repeatmasker/rmouttogff3/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
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| { | ||
| "sarscov2 - genome - fasta - repeatmasker - out - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,d6620b9419b24f5807b1335468594601" | ||
| ], | ||
| "gff3": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,d6620b9419b24f5807b1335468594601" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.3" | ||
| }, | ||
| "timestamp": "2024-08-07T12:41:49.415629" | ||
| }, | ||
| "sarscov2 - genome - fasta - repeatmasker - out": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff3:md5,5c991b62d99cf84149c1d1e90efa4f99" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,d6620b9419b24f5807b1335468594601" | ||
| ], | ||
| "gff3": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff3:md5,5c991b62d99cf84149c1d1e90efa4f99" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,d6620b9419b24f5807b1335468594601" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.3" | ||
| }, | ||
| "timestamp": "2024-08-07T12:42:58.865985" | ||
| } | ||
| } |