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Merge pull request #74 from EBI-Metagenomics/add_goslims_swf
Add goslims subworkflow
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,42 @@ | ||
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| include { GENERATEGAF } from '../../../modules/ebi-metagenomics/generategaf/main' | ||
| include { OWLTOOLS } from '../../../modules/ebi-metagenomics/owltools/main' | ||
| include { SUMMARISEGOSLIMS } from '../../../modules/ebi-metagenomics/summarisegoslims/main' | ||
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| workflow GOSLIM_SWF { | ||
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| take: | ||
| ch_ips // channel: [ val(meta), path(tsv) ] | ||
| go_obo // channel: path(obo) | ||
| goslim_ids // channel: path(txt) | ||
| go_banding // channel: path(txt) | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| GENERATEGAF( ch_ips ) | ||
| ch_versions = ch_versions.mix(GENERATEGAF.out.versions.first()) | ||
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| OWLTOOLS ( | ||
| GENERATEGAF.out.gaf, | ||
| go_obo, | ||
| goslim_ids | ||
| ) | ||
| ch_versions = ch_versions.mix(OWLTOOLS.out.versions.first()) | ||
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| SUMMARISEGOSLIMS ( | ||
| ch_ips, | ||
| OWLTOOLS.out.gaf, | ||
| go_obo, | ||
| go_banding | ||
| ) | ||
| ch_versions = ch_versions.mix(SUMMARISEGOSLIMS.out.versions.first()) | ||
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| emit: | ||
| go_summary = SUMMARISEGOSLIMS.out.go_summary // channel: [ val(meta), path(csv) ] | ||
| goslim_summary = SUMMARISEGOSLIMS.out.goslim_summary // channel: [ val(meta), path(csv) ] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
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| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json | ||
| name: "goslim_swf" | ||
| description: Get GO term and GO-slim term counts out of an InterProScan .tsv output file | ||
| keywords: | ||
| - GO | ||
| - GO-slim | ||
| - interpro | ||
| - interproscan | ||
| - owltools | ||
| components: | ||
| - generategaf | ||
| - owltools | ||
| - summarisegoslims | ||
| input: | ||
| - ch_ips: | ||
| type: file | ||
| description: | | ||
| The input channel containing the InterProScan output file | ||
| Structure: [ val(meta), path(tsv) ] | ||
| pattern: "*.tsv" | ||
| - go_obo: | ||
| type: file | ||
| description: Gene ontology .OBO file, for example go-basic. Can usually be downloaded here https://geneontology.org/docs/download-ontology/ | ||
| pattern: "*.go" | ||
| - goslim_ids: | ||
| type: file | ||
| description: txt file containing the GO terms that make up the input GO-slim | ||
| pattern: "*.txt" | ||
| - go_banding: | ||
| type: file | ||
| description: txt file containing the GO terms and descriptions that make up the input GO-slim | ||
| pattern: "*.txt" | ||
| output: | ||
| - go_summary: | ||
| type: file | ||
| description: | | ||
| Channel containing GO term counts | ||
| Structure: [ val(meta), path(csv) ] | ||
| pattern: "*_summary.csv" | ||
| - goslim_summary: | ||
| type: file | ||
| description: | | ||
| Channel containing GO-slim term counts | ||
| Structure: [ val(meta), path(csv) ] | ||
| pattern: "*_slim.csv" | ||
| - versions: | ||
| type: file | ||
| description: | | ||
| File containing software versions | ||
| Structure: [ path(versions.yml) ] | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@chrisata" | ||
| maintainers: | ||
| - "@chrisata" |
39 changes: 39 additions & 0 deletions
39
subworkflows/ebi-metagenomics/goslim_swf/tests/main.nf.test
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| nextflow_workflow { | ||
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| name "Test Subworkflow GOSLIM_SWF" | ||
| script "../main.nf" | ||
| workflow "GOSLIM_SWF" | ||
| config "./nextflow.config" | ||
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| tag "subworkflows" | ||
| tag "subworkflows_ebimetagenomics" | ||
| tag "subworkflows/goslim_swf" | ||
| tag "generategaf" | ||
| tag "owltools" | ||
| tag "summarisegoslims" | ||
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| test("goslim_swf") { | ||
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| when { | ||
| workflow { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file("${baseDir}/modules/ebi-metagenomics/generategaf/tests/ips_out.tsv", checkIfExists: true) | ||
| ] | ||
| input[1] = file("${baseDir}/modules/ebi-metagenomics/owltools/tests/go-dummy.obo", checkIfExists: true) | ||
| input[2] = file("${baseDir}/modules/ebi-metagenomics/owltools/tests/goslim_ids.txt", checkIfExists: true) | ||
| input[3] = file("${baseDir}/modules/ebi-metagenomics/summarisegoslims/tests/goslim_banding_2024.txt", checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot(workflow.out).match()} | ||
| ) | ||
| } | ||
| } | ||
| } |
59 changes: 59 additions & 0 deletions
59
subworkflows/ebi-metagenomics/goslim_swf/tests/main.nf.test.snap
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| { | ||
| "goslim_swf": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| "versions.yml:md5,9803d78712ef1091ff5f785e34209e66", | ||
| "versions.yml:md5,db47fe42ea02f1cd3ecc4074727e8972", | ||
| "versions.yml:md5,f7674bdfeee9a4d98dbb33e474dd7a68" | ||
| ], | ||
| "go_summary": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_summary.csv:md5,ddf9aa47da0a848795fffb56d9ac3c96" | ||
| ] | ||
| ], | ||
| "goslim_summary": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_summary_slim.csv:md5,ce50e0507a12ef0d70bd41b14926c5d5" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,9803d78712ef1091ff5f785e34209e66", | ||
| "versions.yml:md5,db47fe42ea02f1cd3ecc4074727e8972", | ||
| "versions.yml:md5,f7674bdfeee9a4d98dbb33e474dd7a68" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.4" | ||
| }, | ||
| "timestamp": "2025-01-28T22:32:17.095895573" | ||
| } | ||
| } |
7 changes: 7 additions & 0 deletions
7
subworkflows/ebi-metagenomics/goslim_swf/tests/nextflow.config
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| process{ | ||
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| withName: OWLTOOLS { | ||
| ext.args = '--map2slim' | ||
| } | ||
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| } |