Merge pull request #11 from phac-nml/metadata-irida-output

Metadata irida output
phac-nml · Jun 12, 2024 · d338bd1 · d338bd1
2 parents b353f27 + 7d107b7
commit d338bd1
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Showing 2 changed files with 22 additions and 8 deletions.
diff --git a/conf/iridanext.config b/conf/iridanext.config
@@ -7,13 +7,23 @@ iridanext {
             global = [
             ]
             samples = [
-                "**/**/detailed_summary.tsv",
-                "**/**/mlst.tsv",
-                "**/**/plasmidfinder.tsv",
-                "**/**/resfinder.tsv",
-                "**/**/results.xlsx",
-                "**/**/settings.txt",
-                "**/**/summary.tsv"]
+                "**/detailed_summary.tsv",
+                "**/mlst.tsv",
+                "**/plasmidfinder.tsv",
+                "**/resfinder.tsv",
+                "**/results.xlsx",
+                "**/settings.txt",
+                "**/summary.tsv"]
+        }
+        metadata {
+            samples {
+            csv {
+                path = "**/summary.tsv"
+                sep = "\t"
+                idcol = "Isolate ID"
+            }
         }
     }
 }
+    }
+
diff --git a/modules/local/staramr/main.nf b/modules/local/staramr/main.nf
@@ -29,17 +29,21 @@ process STARAMR_SEARCH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_gzipped = contigs.getName().endsWith(".gz") ? true : false
     def genome_uncompressed_name = contigs.getName().replace(".gz", "")
+    def genome_filename = "${meta.id}.fasta"
     """
     if [ "$is_gzipped" = "true" ]; then
         gzip -c -d $contigs > $genome_uncompressed_name
     fi
 
+    #Change name of input genome to allow irida-next output of metadata
+    mv $genome_uncompressed_name $genome_filename
+
     staramr \\
         search \\
         $args \\
         --nprocs $task.cpus \\
         -o ${prefix}_results \\
-        $genome_uncompressed_name
+        $genome_filename
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":