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Fixes ahead of 1.4.1 release. #431

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Merged
yumisims merged 1 commit into from
Aug 22, 2025
Merged

Fixes ahead of 1.4.1 release. #431

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2 changes: 1 addition & 1 deletion subworkflows/local/hic_mapping/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ workflow HIC_MAPPING {
//
// LOGIC: MAKE YAHS INPUT
//
ref_yahs.map { meta, ref -> ref }.set{ch_ref}
reference_tuple.map { meta, ref -> ref }.set{ch_ref}
reference_index.map { meta, fai -> fai }.set{ch_fai}

//
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4 changes: 2 additions & 2 deletions workflows/treeval.nf
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Expand Up @@ -96,15 +96,15 @@ workflow TREEVAL {
log.info "[Treeval: Info] PROCESSES TO RUN INCLUDE: $include_workflow_steps"

// Validate that all requested steps are valid
def invalid_steps = exclude_steps_list - all_steps_list
invalid_steps = exclude_steps_list - all_steps_list
if (invalid_steps) {
log.error "[Treeval: Error] Invalid step(s) specified in --steps: ${invalid_steps.join(", ")}"
log.error "[Treeval: Error] Valid options are: ${all_steps_list.join(", ")}"
System.exit(1)
}

// Validate that include_workflow_steps contains only valid steps (safety check)
def invalid_include_steps = include_workflow_steps - all_steps_list
invalid_include_steps = include_workflow_steps - all_steps_list
if (invalid_include_steps) {
log.error "[Treeval: Error] Internal error - invalid workflow steps detected: ${invalid_include_steps.join(", ")}"
System.exit(1)
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