Merge pull request #123 from EBI-Metagenomics/feature/optional-parse-…

…results Prase.nf results are optional.
EBI-Metagenomics · May 7, 2024 · d166936 · d166936
2 parents 6483cbf + b88517b
commit d166936
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/bin/parse_viral_pred.py b/bin/parse_viral_pred.py
@@ -300,7 +300,7 @@ def main(pprmeta, finder, sorter, assembly, outdir, prefix=False):
             " in the analysed metagenomic assembly",
             file=sys.stderr,
         )
-        exit(1)
+        exit(0)
 
 
 if __name__ == "__main__":

diff --git a/nextflow/modules/parse.nf b/nextflow/modules/parse.nf
@@ -1,9 +1,8 @@
 process parse {
-      errorStrategy { task.exitStatus = 1 ? 'ignore' :  'terminate' }
-      publishDir "${params.output}/${name}/", mode: 'copy', pattern: "*.fna"
-      publishDir "${params.output}/${name}/", mode: 'copy', pattern: "virsorter_metadata.tsv"
-      publishDir "${params.output}/${name}/${params.finaldir}/", mode: 'copy', pattern: "${name}_virus_predictions.log"
-      label 'python3'
+    publishDir "${params.output}/${name}/", mode: 'copy', pattern: "*.fna"
+    publishDir "${params.output}/${name}/", mode: 'copy', pattern: "virsorter_metadata.tsv"
+    publishDir "${params.output}/${name}/${params.finaldir}/", mode: 'copy', pattern: "${name}_virus_predictions.log"
+    label 'python3'
 
     input:
       tuple val(name), file(fasta), val(contig_number), file(virfinder), file(virsorter), file(pprmeta)
@@ -12,7 +11,7 @@ process parse {
       contig_number.toInteger() > 0 
 
     output:
-      tuple val(name), file("*.fna"), file('virsorter_metadata.tsv'), file("${name}_virus_predictions.log")
+      tuple val(name), file("*.fna"), file('virsorter_metadata.tsv'), file("${name}_virus_predictions.log"), optional: true
 
     script:
     """
-Original file line number
+Diff line change
@@ Expand Up @@
                 " in the analysed metagenomic assembly",
                 file=sys.stderr,
             )
-            exit(1)
+            exit(0)
     if __name__ == "__main__":
@@ Expand Down @@