From ae22d57e9d2ae4445a68e0645de958e29220954b Mon Sep 17 00:00:00 2001
From: Charles Plessy <charles.plessy@oist.jp>
Date: Wed, 19 Jun 2024 14:52:05 +0900
Subject: [PATCH] Fix file names in modules runnign on single genomes.

---
 main.nf                      | 5 +----
 workflows/pairgenomealign.nf | 4 ++++
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index bbc609f..e220d45 100644
--- a/main.nf
+++ b/main.nf
@@ -91,14 +91,11 @@ workflow {
         .map { file_obj -> [ [id:params.targetName], file_obj] }
         .set { ch_target }
 
-    ch_query = PIPELINE_INITIALISATION.out.samplesheet
-        .map { row -> [ [id: params.targetName + '___' + row[0].id] , row.tail() ] }
-
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_PAIRGENOMEALIGN (
-        ch_query,
+        PIPELINE_INITIALISATION.out.samplesheet,
         ch_target
     )
 
diff --git a/workflows/pairgenomealign.nf b/workflows/pairgenomealign.nf
index bc76f6a..ba7c0f4 100644
--- a/workflows/pairgenomealign.nf
+++ b/workflows/pairgenomealign.nf
@@ -55,6 +55,10 @@ workflow PAIRGENOMEALIGN {
     ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLYSCAN.out.json.collect{it[1]})
     ch_versions = ch_versions.mix(ASSEMBLYSCAN.out.versions.first())
 
+    // Prefix id with target genome name before producing alignment files
+    ch_samplesheet = ch_samplesheet
+        .map { row -> [ [id: params.targetName + '___' + row[0].id] , row.tail() ] }
+
     //
     // SUBWORKFLOW: pairalign_m2o
     //