add cancer splicing lib to starfusion ref #610
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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: 3.1.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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rannick
reviewed
Jan 21, 2025
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@rannick something seems wrong with the |
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I would like to understand what is going on before merging, hope that is ok with you. Just easier to debug if there are not multiple layers |
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Yeah I fully understand! This is not urgent for us I updated our local reference manually. Let me know if I can help |
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I think the error comes from the starfusion references being different |
atrigila
reviewed
Jan 22, 2025
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Right! I forgot thanks for the reminder :)
atrigila
reviewed
Jan 22, 2025
| @@ -142,7 +143,15 @@ workflow BUILD_REFERENCES { | |||
| !file(params.starfusion_ref_stub_check).exists() || file(params.starfusion_ref_stub_check).isEmpty() )) { | |||
| STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species) | |||
| ch_versions = ch_versions.mix(STARFUSION_BUILD.out.versions) | |||
| ch_starfusion_ref = STARFUSION_BUILD.out.reference | |||
| if (params.ctatsplicing || params.all) { | |||
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Suggested change
| if (params.ctatsplicing || params.all) { | |
| if (params.ctatsplicing) { |
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The params.all is in the outer if clause:
if ((params.starfusion || params.all) &&
(!file(params.starfusion_ref).exists() || file(params.starfusion_ref).isEmpty() ||
!file(params.starfusion_ref_stub_check).exists() || file(params.starfusion_ref_stub_check).isEmpty() )) {
STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species)
I think that is why the test_build is failing. It is not populating the ch_starfusion_ref with CTATSPLICING_PREPGENOMELIB.out.reference or STARFUSION_BUILD.out.reference
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Hmm but the ctatsplicing reference creation will not run if --all is supplied this way?
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I think it is difficult to differentiate which is the default here. If --all is supplied, should ch_starfusion_ref produce STARFUSION_BUILD.out.reference or CTATSPLICING_PREPGENOMELIB.out.reference?
Before adding your new module CTATSPLICING_PREPGENOMELIB, the default for --all was to use the STARFUSION_BUILD.out.reference but now it will always default to CTATSPLICING_PREPGENOMELIB.out.reference.
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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).