split_assembly module's output is now optional

Author: cimendes

flowcraft/generator/templates/split_assembly.nf

@@ -18,7 +18,7 @@ process split_assembly_{{ pid }} {
     val min_contig_size from IN_min_contig_size_{{ pid }}
 
     output:
-    file '*split.fasta' into splitCh_{{ pid }}
+    file '*split.fasta' into splitCh_{{ pid }} optional true
     {% with task_name="split_assembly" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}

flowcraft/generator/templates/viral_assembly.nf

@@ -60,7 +60,7 @@ process va_spades_{{ pid }} {
     val clear from checkpointClear_{{ pid }}
 
     output:
-    set sample_id, file({task.exitStatus == 1 ? ".exitcodeU" : '*_spades*.fasta'}) into assembly_spades
+    set sample_id, file({task.exitStatus == 1 ? ".exitcode" : '*_spades*.fasta'}) into assembly_spades
     {% with task_name="va_spades" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}