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Fix ctatsplicing ref building trigger #716

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Fix ctatsplicing ref building trigger #716

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d00fdc0
change logic for triggering ctatsplicing ref building
rannick Jul 17, 2025
f42a90c
add arriba fix
rannick Jul 17, 2025
159696a
update schema
rannick Jul 17, 2025
45c865f
no reliance on starfusion if it was run ahead for example
rannick Jul 17, 2025
ba8b150
add ctatsplicing ref to schema
rannick Jul 17, 2025
e67bd20
Merge branch 'dev' into fix_ctatsplicing_ref_building_trigger
rannick Aug 25, 2025
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6 changes: 6 additions & 0 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,12 @@
"fa_icon": "far fa-file-code",
"description": "Path to arriba output"
},
"ctatsplicing_ref": {
"type": "string",
"format": "directory-path",
"fa_icon": "far fa-file-code",
"description": "Path to ctatsplicing references"
},
"download_refs": {
"type": "boolean",
"fa_icon": "far fa-file-code",
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24 changes: 11 additions & 13 deletions subworkflows/local/build_references/main.nf
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Expand Up @@ -146,7 +146,10 @@ workflow BUILD_REFERENCES {

def ch_starfusion_ref = Channel.empty()
if (tools.intersect(["starfusion", "ctatsplicing", "fusioninspector"])) {
if (!exists_not_empty(params.starfusion_ref)) {
if (exists_not_empty(params.starfusion_ref)) {
ch_starfusion_ref = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it] }
}
else {
if(!params.fusion_annot_lib) {
error("Expected --fusion_annot_lib to be specified when using StarFusion or any tools that depend on it")
}
Expand Down Expand Up @@ -178,19 +181,14 @@ workflow BUILD_REFERENCES {

STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species, pfam_file, dfam_urls_ch, params.annot_filter_url)
ch_versions = ch_versions.mix(STARFUSION_BUILD.out.versions)
if (tools.contains("ctatsplicing")) {
CTATSPLICING_PREPGENOMELIB(
STARFUSION_BUILD.out.reference,
params.ctatsplicing_cancer_introns
)
ch_versions = ch_versions.mix(CTATSPLICING_PREPGENOMELIB.out.versions)
ch_starfusion_ref = CTATSPLICING_PREPGENOMELIB.out.reference
} else {
ch_starfusion_ref = STARFUSION_BUILD.out.reference
}
}
else {
ch_starfusion_ref = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it] }
if (tools.contains("ctatsplicing") && !exists_not_empty(params.ctatsplicing_ref)) {
CTATSPLICING_PREPGENOMELIB(
ch_starfusion_ref,
params.ctatsplicing_cancer_introns
)
ch_versions = ch_versions.mix(CTATSPLICING_PREPGENOMELIB.out.versions)
ch_starfusion_ref = CTATSPLICING_PREPGENOMELIB.out.reference
}
}

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