Reintegrate STARFUSION_BUILD module#709
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delfiterradas merged 19 commits intonf-core:devfrom Jul 23, 2025
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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atrigila
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Jul 17, 2025
nextflow_schema.json
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| "dfam_h3i": { | ||
| "type": "string", | ||
| "format": "uri", | ||
| "pattern": "^https?://.*", |
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A question: people might have these files downloaded or they might host their files in places other than https (such as s3) so I would remove this pattern for all the dfam files. However, you can add a pattern for the required suffix (for example .h3i `.h3f``)
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I agree, I'll change that :)
atrigila
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Jul 17, 2025
| dfam_h3i = Channel.fromPath(params.dfam_h3i, checkIfExists: true) | ||
| dfam_h3m = Channel.fromPath(params.dfam_h3m, checkIfExists: true) | ||
| dfam_h3p = Channel.fromPath(params.dfam_h3p, checkIfExists: true) | ||
| } else { |
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I would change this for an else if dfam_version and params.species, then an else for failure if all those are missing.
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@delfiterradas is this addressed because dfam_h** are dependent on dfam_version and species?
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Yes, now dfam_h** by default are dependent on the dfam_version and species. However, the user can instead pass the full paths to each of the dfam_h** params and in that case it does not use the dfam_version.
| } | ||
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| if ((params.dfam_hmm || params.dfam_h3p || params.dfam_h3m || params.dfam_h3i || params.dfam_h3f) && (params.dfam_version)) { | ||
| log.warn("Both custom dfam_urls and dfam_version were specified. \n If you want to use custom dfam URLs make sure to provide the full paths for each of the dfam params as the dfam_version will not be overwritten. \n Otherwise, use only the `--dfam_version` and `--species` params and the dfam URLs will be automatically filled.") |
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This warning should tell you which of the two options was preferred. In your if/else if these parameters are provided: params.dfam_hmm params.dfam_h3p params.dfam_h3m params.dfam_h3i params.dfam_h3f, then the "building" of the URL via dfam_version won't be triggered. So it should make it clear here.
rannick
reviewed
Jul 18, 2025
nextflow.config
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| starindex_ref = "${params.genomes_base}/star" | ||
| fusionreport_ref = "${params.genomes_base}/fusion_report_db" | ||
| ctatsplicing_cancer_introns = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz" | ||
| dfam_hmm = null |
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For consistency: I would put all the defaults in nextflow.config rather than nextflow_schema.json since it is the primary source
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The defaults should be in both (otherwise linting will complain). The schema defaults will be mainly used for documentation and the config defaults will be used as the real defaults
rannick
reviewed
Jul 18, 2025
rannick
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Jul 18, 2025
nvnieuwk
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Jul 18, 2025
apeltzer
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Jul 23, 2025
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apeltzer
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From my end, this looks good and reasonable 👍🏻
rannick
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Jul 23, 2025
| dfam_h3i = Channel.fromPath(params.dfam_h3i, checkIfExists: true) | ||
| dfam_h3m = Channel.fromPath(params.dfam_h3m, checkIfExists: true) | ||
| dfam_h3p = Channel.fromPath(params.dfam_h3p, checkIfExists: true) | ||
| } else { |
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@delfiterradas is this addressed because dfam_h** are dependent on dfam_version and species?
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Closes #694
PR checklist
nf-core lint).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).