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Added parameter filter_genes_by_aa_length
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::agat=1.4.2" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| process AGAT_SPFILTERBYORFSIZE { | ||
| tag "$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' }" | ||
|
|
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| input: | ||
| tuple val(meta), path(gxf) | ||
| path config | ||
|
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| output: | ||
| tuple val(meta), path("*.passed.gff") , emit: passed_gff | ||
| tuple val(meta), path("*.failed.gff") , emit: failed_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" in [ "${prefix}.passed.gff", "${prefix}.failed.gff" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| agat_sp_filter_by_ORF_size.pl \\ | ||
| -g $gxf \\ | ||
| $args \\ | ||
| $config_arg \\ | ||
| -o $prefix | ||
| mv \\ | ||
| ${prefix}_NOT* \\ | ||
| "${prefix}.failed.gff" | ||
| mv \\ | ||
| ${prefix}_* \\ | ||
| "${prefix}.passed.gff" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_flag_short_introns.pl -h | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| if( "$gxf" in [ "${prefix}.passed.gff", "${prefix}.failed.gff" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | ||
| """ | ||
| touch ${prefix}.passed.gff | ||
| touch ${prefix}.failed.gff | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| agat: \$(agat_sp_flag_short_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 +1,67 @@ | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "agat_spfilterbyorfsize" | ||
| description: The script reads a gff annotation file, and create two output files, | ||
| one contains the gene models with ORF passing the test, the other contains the rest. | ||
| By default the test is "> 100" that means all gene models that have ORF longer than | ||
| 100 Amino acids, will pass the test. | ||
| keywords: | ||
| - genomics | ||
| - GFF/GTF | ||
| - filter | ||
| - annotation | ||
| 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/" | ||
| 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:'sample1' ]` | ||
| - 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: | ||
| - passed_gff: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ] | ||
| - "*.passed.gff": | ||
| type: file | ||
| description: GFF file with gene models which pass the filter test | ||
| - failed_gff: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ] | ||
| - "*.failed.gff": | ||
| type: file | ||
| description: GFF file with remaining gene models | ||
| - 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 +1,62 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process AGAT_SPFILTERBYORFSIZE" | ||
| script "../main.nf" | ||
| process "AGAT_SPFILTERBYORFSIZE" | ||
|
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||
| tag "modules" | ||
| tag "modules_gallvp" | ||
| tag "agat" | ||
| tag "agat/spfilterbyorfsize" | ||
|
|
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| test("actinidia_chinensis - genome - gtf") { | ||
|
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|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz', 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' ], // 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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||
|
|
||
| } |
100 changes: 100 additions & 0 deletions
100
modules/gallvp/agat/spfilterbyorfsize/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| { | ||
| "homo_sapiens - genome - gtf - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.passed.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.failed.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| "versions.yml:md5,bc298e3688f3f90f287f56ee6929bd29" | ||
| ], | ||
| "failed_gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.failed.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "passed_gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.passed.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,bc298e3688f3f90f287f56ee6929bd29" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-12-10T17:07:11.619928" | ||
| }, | ||
| "actinidia_chinensis - genome - gtf": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.passed.gff:md5,e2558c89e50df32d654f19f9a69e46a3" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.failed.gff:md5,d7eb6ae1c3dc30675138029b513073eb" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| "versions.yml:md5,bc298e3688f3f90f287f56ee6929bd29" | ||
| ], | ||
| "failed_gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.failed.gff:md5,d7eb6ae1c3dc30675138029b513073eb" | ||
| ] | ||
| ], | ||
| "passed_gff": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.passed.gff:md5,e2558c89e50df32d654f19f9a69e46a3" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,bc298e3688f3f90f287f56ee6929bd29" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-12-10T17:07:06.829402" | ||
| } | ||
| } |
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