- in the viral_assembly module, if the assembly fails in spades it now tries with megahit

- spades template now reports spades' exit code if the run fails

Author: cimendes

changelog.md

@@ -32,6 +32,7 @@ error when it is set to `null`.
 - Fixed minor issue preventing the `maxbin2` and `split_assembly` components 
 from being used multiples times in a pipeline
 - Added a catch to the `filter_poly` process for cases where the input file is empty. 
+- spades template now reports the exit code of spades' execution
 
 ### Bug fixes
 

flowcraft/generator/templates/viral_assembly.nf

@@ -48,6 +48,8 @@ process va_spades_{{ pid }} {
     // Send POST request to platform
     {% include "post.txt" ignore missing %}
 
+    validExitStatus 0,1
+
     tag { sample_id }
     publishDir 'results/assembly/spades_{{ pid }}/', pattern: '*_spades*.fasta', mode: 'copy'
 
@@ -58,7 +60,7 @@ process va_spades_{{ pid }} {
     val clear from checkpointClear_{{ pid }}
 
     output:
-    set sample_id, file('*_spades*.fasta') into assembly_spades
+    set sample_id, file({task.exitStatus == 1 ? ".exitcodeU" : '*_spades*.fasta'}) into assembly_spades
     {% with task_name="va_spades" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}
@@ -71,13 +73,10 @@ process va_spades_{{ pid }} {
 class VerifyCompletness {
 
     public static boolean contigs(String filename, int threshold){
-        println(filename)
         BufferedReader reader = new BufferedReader(new FileReader(filename));
         boolean result = processContigs(reader, threshold);
         reader.close()
 
-        println(result)
-
         return result;
     }
 
@@ -91,7 +90,6 @@ class VerifyCompletness {
                 splittedLine = line.split('_')
                 lineThreshold = splittedLine[3].toInteger()
                 if(lineThreshold >= threshold) {
-                    println(lineThreshold)
                     return true;
                 }
              }
@@ -103,7 +101,7 @@ class VerifyCompletness {
 
 megahit = Channel.create()
 good_assembly = Channel.create()
-assembly_spades.choice(good_assembly, megahit){a -> VerifyCompletness.contigs(a[1].toString(), params.minimumContigSize{{ param_id }}.toInteger()) == true ? 0 : 1}
+assembly_spades.choice(good_assembly, megahit){a -> a[1].toString() == "null" ? false : VerifyCompletness.contigs(a[1].toString(), params.minimumContigSize{{ param_id }}.toInteger()) == true ? 0 : 1}
 
 
 process va_megahit_{{ pid }}  {

flowcraft/templates/spades.py

@@ -48,6 +48,7 @@
 __template__ = "spades-nf"
 
 import os
+import sys
 import re
 import subprocess
 
@@ -239,7 +240,7 @@ def main(sample_id, fastq_pair, max_len, kmer, opts, clear):
     with open(".status", "w") as fh:
         if p.returncode != 0:
             fh.write("error")
-            return
+            sys.exit(p.returncode)
         else:
             fh.write("pass")