feat: remove hacky INDEX

nf-core · Jan 20, 2022 · f524d06 · f524d06
1 parent 37c5cb4
commit f524d06
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Showing 4 changed files with 10 additions and 13 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:
-    path "bwa"         , emit: index
-    path "versions.yml", emit: versions
+    tuple val("bwa/${fasta.baseName}"), 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)
-    path  index
+    tuple val(index_path), path(index)
     val   sort_bam
 
     output:
@@ -23,13 +23,11 @@ process BWA_MEM {
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa mem \\
         $args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        $index_path \\
         $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:
-    path "bwamem2"      , emit: index
-    path "versions.yml" , emit: versions
+    tuple val("bwamem2/${fasta}"), path("bwamem2"), emit: index
+    path "versions.yml"                           , emit: versions
 
     script:
     def args = task.ext.args ?: ''
@@ -21,7 +21,8 @@ process BWAMEM2_INDEX {
     bwa-mem2 \\
         index \\
         $args \\
-        $fasta -p bwamem2/${fasta}
+        -p bwamem2/${fasta} \\
+        $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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)
-    path  index
+    tuple val(index_path), path(index)
     val   sort_bam
 
     output:
@@ -23,14 +23,12 @@ process BWAMEM2_MEM {
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa-mem2 \\
         mem \\
         $args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        $index_path \\
         $reads \\
         | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -