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Merge pull request #12 from GallVp/gxf_fasta_agat_spaddintrons_spextr…
…actsequences Added gxf_fasta_agat_spaddintrons_spextractsequences
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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: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| name: "agat_spaddintrons" | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - "bioconda::agat=1.4.0" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| process AGAT_SPADDINTRONS { | ||
| tag "$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:1.4.0--pl5321hdfd78af_0' : | ||
| 'biocontainers/agat:1.4.0--pl5321hdfd78af_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(gxf) | ||
| path config | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.gff") , emit: gff | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| 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_arg = config ? "-c $config" : '' | ||
| if( "$gxf" == "${prefix}.gff" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| agat_sp_add_introns.pl \\ | ||
| $args \\ | ||
| -g $gxf \\ | ||
| $config_arg \\ | ||
| -o ${prefix}.gff | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_add_introns.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| if( "$gxf" == "${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_add_introns.pl -h | 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 +1,55 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "agat_spaddintrons" | ||
| description: | | ||
| The script aims to add intron features to gtf/gff file without intron features. | ||
| keywords: | ||
| - genomics | ||
| - gff | ||
| - gtf | ||
| - add | ||
| - intron | ||
| - 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_add_introns.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 ]` | ||
| - gxf: | ||
| type: file | ||
| description: Input GFF3/GTF file | ||
| pattern: "*.{gff,gff3,gtf}" | ||
| - 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" | ||
|
|
||
| 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" | ||
|
|
||
| authors: | ||
| - "@GallVp" | ||
| maintainers: | ||
| - "@GallVp" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process AGAT_SPADDINTRONS" | ||
| script "../main.nf" | ||
| process "AGAT_SPADDINTRONS" | ||
|
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| tag "modules" | ||
| tag "modules_gallvp" | ||
| tag "agat" | ||
| tag "agat/spaddintrons" | ||
|
|
||
| test("homo_sapiens - genome - gtf") { | ||
|
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||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.gtf', checkIfExists: true) | ||
| ] | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("homo_sapiens - genome - gtf - stub") { | ||
|
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| options '-stub' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.gtf', checkIfExists: true) | ||
| ] | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "homo_sapiens - genome - gtf - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,480dfe983a8b4469c1dff8b7a08d855d" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,480dfe983a8b4469c1dff8b7a08d855d" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-06-24T16:22:13.888389" | ||
| }, | ||
| "homo_sapiens - genome - gtf": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,a798830c6ad0a27b1564b98e1a1fc3aa" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,480dfe983a8b4469c1dff8b7a08d855d" | ||
| ], | ||
| "gff": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.gff:md5,a798830c6ad0a27b1564b98e1a1fc3aa" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,480dfe983a8b4469c1dff8b7a08d855d" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-06-24T15:21:51.693488" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| agat/spaddintrons: | ||
| - "modules/pfr/agat/spaddintrons/**" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| name: "agat_spextractsequences" | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - bioconda::agat=1.4.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| process AGAT_SPEXTRACTSEQUENCES { | ||
| tag "$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:1.4.0--pl5321hdfd78af_0' : | ||
| 'biocontainers/agat:1.4.0--pl5321hdfd78af_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(gxf) | ||
| path fasta | ||
| path config | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.fasta") , emit: fasta | ||
| 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}" | ||
| def config_arg = config ? "-c $config" : '' | ||
| if( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| agat_sp_extract_sequences.pl \\ | ||
| $args \\ | ||
| -g $gxf \\ | ||
| -f $fasta \\ | ||
| $config_arg \\ | ||
| -o ${prefix}.fasta | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_extract_sequences.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| if( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| touch ${prefix}.fasta | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_extract_sequences.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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