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Add validation error for incompatible transcript_fasta and additional_fasta params #1633

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Merged
pinin4fjords merged 3 commits into from
Nov 25, 2025
+10 −7
Merged

Add validation error for incompatible transcript_fasta and additional_fasta params #1633

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Copilot Nov 25, 2025
d43f0da
Fix validation: check only the relevant pseudo-aligner index
Copilot Nov 25, 2025
81bda46
Refactor: use else-if structure for pseudo-aligner check
Copilot Nov 25, 2025
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17 changes: 10 additions & 7 deletions subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -267,13 +267,16 @@ def validateInputParameters() {
// (i.e., no pre-built salmon/kallisto index provided). If the user provides a pre-built
// index that already contains the spike-ins, the combination is valid.
if (params.additional_fasta) {
def building_pseudo_index = (
!params.skip_pseudo_alignment &&
params.pseudo_aligner &&
!params.salmon_index &&
!params.kallisto_index
)
if (building_pseudo_index) {
def needs_to_build_index = false
if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
// Check if the relevant index for the selected pseudo-aligner is missing
if (params.pseudo_aligner == 'salmon' && !params.salmon_index) {
needs_to_build_index = true
} else if (params.pseudo_aligner == 'kallisto' && !params.kallisto_index) {
needs_to_build_index = true
}
}
if (needs_to_build_index) {
transcriptFastaAdditionalFastaError()
}
}
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