Commit 7f018592 authored by aknecht2's avatar aknecht2
Browse files

Updated yaml files to mark final_output. Final output implies both...

Updated yaml files to mark final_output.  Final output implies both transfer=true and should_save=true
parent 20909661
......@@ -131,3 +131,4 @@ align:
outputs:
- align.bam:
type: file
final_result: true
......@@ -26,17 +26,16 @@ peak_call:
outputs:
- region_sorted.bed:
type: file
save_result: true
transfer: true
final_result: true
- peakranger_format_bed:
inputs:
- summit.bed:
type: file
additional_inputs: null
outputs:
- results_sorted.bed:
- summit_sorted.bed:
type: file
transfer: true
final_result: true
- ccat[tool]:
- ccat_callpeak:
inputs:
......@@ -72,17 +71,16 @@ peak_call:
outputs:
- region_sorted.bed:
type: file
save_result: true
transfer: true
final_result: true
- ccat_format_bed:
inputs:
- significant.peak:
type: file
additional_inputs: null
outputs:
- results_sorted.bed:
- peak_sorted.bed:
type: file
transfer: true
final_result: true
- gem[tool]:
- gem_callpeak:
inputs:
......@@ -116,8 +114,7 @@ peak_call:
outputs:
- results_GEM_sorted.bed:
type: file
save_result: true
transfer: true
final_result: true
- sort_awk_sort_peaks:
inputs:
- GPS_events.narrowPeak:
......@@ -126,7 +123,7 @@ peak_call:
outputs:
- results_GPS_sorted.bed:
type: file
transfer: true
final_result: true
- spp[tool]:
- cp:
inputs:
......@@ -166,7 +163,7 @@ peak_call:
outputs:
- results_sorted.bed:
type: file
transfer: true
final_result: true
- macs2[tool]:
- macs2_callpeak:
inputs:
......@@ -192,4 +189,4 @@ peak_call:
outputs:
- results_sorted.bed:
type: file
transfer: true
final_result: true
......@@ -49,3 +49,4 @@ remove_duplicates:
outputs:
- no_dups_chr.bed:
type: file
final_result: true
......@@ -415,7 +415,7 @@ class WorkflowModule(object):
"name": outputs[param_name],
"file": master_files[outputs[param_name]],
"type": param_info["type"],
"transfer": param_info.get("transfer", False)
"transfer": param_info.get("transfer", False) || param_info.get("final_result", False)
})
else:
param_list.append({
......
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