Add the finaletoolkit/delfi module#11547
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This uses FinaleToolkit to calculate the DELFI score (Cristiano et al., 2019). cf. nf-core#11365
SPPearce
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May 8, 2026
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@SPPearce I should've handled it but I need to check the tests here, locally they fail probably because my Nextflow version is too old (error in an unrelated module). EDIT: tests are green. |
SPPearce
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May 11, 2026
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| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true) | ||
| , |
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| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true) | |
| , | |
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true), |
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| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true) | ||
| , |
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| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true) | |
| , | |
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true), |
| assertAll( | ||
| { assert snapshot( | ||
| process.out, | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
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Don't need this if you are capturing process.out in its entirety.
| assertAll( | ||
| { assert snapshot( | ||
| process.out, | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
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| process.out.findAll { key, val -> key.startsWith("versions") } |
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| { assert snapshot( | ||
| process.out, | ||
| process.out.findAll { key, val -> key.startsWith("versions") } | ||
| ).match() } |
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| { assert snapshot( | |
| process.out, | |
| process.out.findAll { key, val -> key.startsWith("versions") } | |
| ).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
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Also applies to the stub.
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| - sort | ||
| - genomics | ||
| - fragmentomics |
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| - bam: | ||
| type: file | ||
| description: Sorted BAM file | ||
| pattern: "*.bam" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_2572" |
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Does this work with cram files?
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Honestly I'm not sure. I'll check the code directly, but it looks like it wants BAM. I'll investigate.
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Many thanks @SPPearce for the review. Most of these show why copy-pasting is bad. ;) |
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PR checklist
This PR introduces support for the
delfisubcommand in finaletoolkit, which calculates the DELFI score, a popular measure used in fragmentomics introduced in Cristiano et al., 2019.References #11365
topic: versions- See version_topicslabelnf-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