EBI MGnify - ENA Genome uploader #9177
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vagkaratzas
reviewed
Oct 9, 2025
| path(fastas, stageAs: "genomes/*") | ||
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| output: | ||
| tuple val(meta), path("upload_output/*") , emit: upload_output_dir |
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Maybe rename to emit: results
This is the pattern I mostly see when outputting whole folders
| """ | ||
| genome_upload \\ | ||
| $args \\ | ||
| --upload_study "${meta.study_accession}" \\ |
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I like the use of meta here, but we will need a second opinion if that's preferred over additional input params
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| input: | ||
| tuple val(meta), path(metadata_tsv) | ||
| path(fastas, stageAs: "genomes/*") |
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', study_accession:'ERP159782', center_name:'nf-core' ]` | ||
| - upload_output/*: |
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Suggested change
| - upload_output/*: | |
| - upload_output: |
| - upload_output/*: | ||
| type: directory | ||
| description: Directory containing all upload outputs | ||
| pattern: "upload_output/*" |
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Suggested change
| pattern: "upload_output/*" | |
| pattern: "*" |
| @@ -0,0 +1,5 @@ | |||
| process { | |||
| withName: 'GENOMEUPLOADER' { | |||
| ext.args = '--mags' | |||
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| ext.args = '--mags' | |
| ext.args = params.module_args |
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| test("genome - fasta - gz") { | ||
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| when { |
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Suggested change
| when { | |
| when { | |
| params { | |
| module_args = '--mags' | |
| } |
| ], | ||
| metadata_file | ||
| ] | ||
| input[1] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/magmap/testdata/GCA_002688505.1_ASM268850v1_genomic.fna.gz', checkIfExists: true) |
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This file will probably need to be deposited in nf-core test-datasets as well
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| { | |||
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I dont see the stub test in the snapshot
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| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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Suggested change
| { assert process.success }, | |
| { assert snapshot(process.out).match() } | |
| { assert process.success }, | |
| { assert snapshot( | |
| process.out.upload_output_dir, | |
| process.out.registered_mags, | |
| process.out.genome_samples, | |
| process.out.manifests, | |
| process.out.versions.collect{ path(it).yaml } | |
| ).match() } |
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda