feat: even better

nf-core · Jan 20, 2022 · 6316357 · 6316357
1 parent f524d06
commit 6316357
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf
@@ -11,8 +11,8 @@ process BWA_INDEX {
     path fasta
 
     output:
-    tuple val("bwa/${fasta.baseName}"), path ("bwa") , emit: index
-    path "versions.yml"                              , emit: versions
+    path "bwa/*"       , emit: index
+    path "versions.yml", emit: versions
 
     script:
     def args = task.ext.args ?: ''

diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf
@@ -9,7 +9,7 @@ process BWA_MEM {
 
     input:
     tuple val(meta), path(reads)
-    tuple val(index_path), path(index)
+    path  index
     val   sort_bam
 
     output:
@@ -27,7 +27,7 @@ process BWA_MEM {
         $args \\
         $read_group \\
         -t $task.cpus \\
-        $index_path \\
+        ${index[0].baseName} \\
         $reads \\
         | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 

diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf
@@ -11,8 +11,8 @@ process BWAMEM2_INDEX {
     path fasta
 
     output:
-    tuple val("bwamem2/${fasta}"), path("bwamem2"), emit: index
-    path "versions.yml"                           , emit: versions
+    path "bwamem2/*"   , emit: index
+    path "versions.yml", emit: versions
 
     script:
     def args = task.ext.args ?: ''

diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf
@@ -9,7 +9,7 @@ process BWAMEM2_MEM {
 
     input:
     tuple val(meta), path(reads)
-    tuple val(index_path), path(index)
+    path  index
     val   sort_bam
 
     output:
@@ -28,7 +28,7 @@ process BWAMEM2_MEM {
         $args \\
         $read_group \\
         -t $task.cpus \\
-        $index_path \\
+        ${index[0].baseName} \\
         $reads \\
         | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -