From 172123f575c3dbf99e340d7717499c42923498c2 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Tue, 11 Jun 2024 14:22:00 -0400
Subject: [PATCH 1/3] Draft: Add metadata in irida-output

---
 conf/iridanext.config         | 24 +++++++++++++++++-------
 modules/local/staramr/main.nf |  5 ++++-
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/conf/iridanext.config b/conf/iridanext.config
index 741ad04..f9d58d6 100644
--- 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
index b8a4614..83bd0c7 100644
--- a/modules/local/staramr/main.nf
+++ b/modules/local/staramr/main.nf
@@ -34,12 +34,15 @@ process STARAMR_SEARCH {
         gzip -c -d $contigs > $genome_uncompressed_name
     fi
 
+    #Change name of input genome to sample name to allow irida-next output of metadata
+    mv $genome_uncompressed_name ${meta.id}
+
     staramr \\
         search \\
         $args \\
         --nprocs $task.cpus \\
         -o ${prefix}_results \\
-        $genome_uncompressed_name
+        $meta.id
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From d7417cb7a4ad9d89cd2048e1e01609c8c39a90cd Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Tue, 11 Jun 2024 20:03:45 -0400
Subject: [PATCH 2/3] Found a misplaced colon keeping meta from populating

---
 conf/iridanext.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/iridanext.config b/conf/iridanext.config
index f9d58d6..5d98809 100644
--- a/conf/iridanext.config
+++ b/conf/iridanext.config
@@ -15,7 +15,7 @@ iridanext {
                 "**/settings.txt",
                 "**/summary.tsv"]
         }
-        metadata: {
+        metadata {
             samples {
             csv {
                 path = "**/summary.tsv"

From 7d107b74dea77c0873ffd11eb3531ce782644f87 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Wed, 12 Jun 2024 15:19:17 -0400
Subject: [PATCH 3/3] Added genome_filename variable for genome used by staramr

---
 modules/local/staramr/main.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/modules/local/staramr/main.nf b/modules/local/staramr/main.nf
index 83bd0c7..788591a 100644
--- a/modules/local/staramr/main.nf
+++ b/modules/local/staramr/main.nf
@@ -29,20 +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 sample name to allow irida-next output of metadata
-    mv $genome_uncompressed_name ${meta.id}
+    #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 \\
-        $meta.id
+        $genome_filename
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":