Migrate STARFUSION_DETECT local module
#8813
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SPPearce
reviewed
Jul 27, 2025
@SPPearce yes! I have added a new test for single end data. Right now the tests are using reads from the STAR-Fusion repository but I will update it when the data is available on nf-core (nf-core/test-datasets#1693). Regarding the files that are downloaded with the |
SPPearce
reviewed
Aug 5, 2025
atrigila
reviewed
Aug 6, 2025
|
@SPPearce should be ready for another review now 👍 |
SPPearce
approved these changes
Aug 8, 2025
| script: | ||
| def prefix = task.ext.prefix ?: "${meta.id}.starfusion" | ||
| def fastq_arg = reads ? (meta.single_end ? "--left_fq ${reads[0]}" : "--left_fq ${reads[0]} --right_fq ${reads[1]}") : "" | ||
| def junction_arg = junction ? "-J ${junction}" : "" |
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Suggested change
| def junction_arg = junction ? "-J ${junction}" : "" | |
| def junction_arg = junction ? "-J ${junction}" : "" |
| tag "$meta.id" | ||
| label 'process_high' | ||
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| conda "${moduleDir}/environment.yml" |
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| conda "${moduleDir}/environment.yml" | |
| // WARN: Incorrect version information provided by tool on CLI. Please update version string below when bumping container versions. | |
| conda "${moduleDir}/environment.yml" |
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| tag "modules_nfcore" | ||
| tag "starfusion/build" | ||
| tag "starfusion" | ||
| tag "starfusion/detect" | ||
| tag "modules" |
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| tag "modules_nfcore" | |
| tag "starfusion/build" | |
| tag "starfusion" | |
| tag "starfusion/detect" | |
| tag "modules" | |
| tag "modules" | |
| tag "modules_nfcore" | |
| tag "starfusion" | |
| tag "starfusion/build" | |
| tag "starfusion/detect" | |
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PR checklist
Closes nf-core/rnafusion#696
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