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Bug Fix: Change to mode param, preventing subworkflow selection. #438

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Merged
weaglesBio merged 3 commits into from
Oct 15, 2025
Merged

Bug Fix: Change to mode param, preventing subworkflow selection. #438

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596b2c3
Merge pull request #437 from sanger-tol/dev
muffato Oct 10, 2025
4a44fc4
fix to mode issue
weaglesBio Oct 15, 2025
acd0400
lint
weaglesBio Oct 15, 2025
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17 changes: 14 additions & 3 deletions workflows/treeval.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -92,9 +92,20 @@ workflow TREEVAL {
// Determine workflow steps based on run mode
// Take processes from the mode's include list, remove any CLI excluded steps
//
include_workflow_steps = mode_include_map.containsKey(mode) ?
(mode_include_map[mode] - exclude_steps_list).unique() :
(all_steps_list - exclude_steps_list).unique()

// Extract the actual value from DataflowVariable if needed
def actual_mode = mode.toString()
if (actual_mode.contains('DataflowVariable')) {
// Extract value from DataflowVariable(value=RAPID_TOL) format
actual_mode = actual_mode.replaceAll('.*DataflowVariable\\(value=', '').replaceAll('\\).*', '')
}

// Determine which workflow steps to run based on mode
if (mode_include_map.containsKey(actual_mode)) {
include_workflow_steps = (mode_include_map[actual_mode] - exclude_steps_list).unique()
} else {
include_workflow_steps = (all_steps_list - exclude_steps_list).unique()
}

// This acts as a "double check" for the user
log.info "[Treeval: Info] PROCESSES TO RUN INCLUDE: $include_workflow_steps"
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