feat: try to improve index

maxulysse · Mar 15, 2021 · 35956ab · 35956ab
1 parent 1cad354
commit 35956ab
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Showing 4 changed files with 9 additions and 13 deletions.
diff --git a/modules/nf-core/software/bwa/index/main.nf b/modules/nf-core/software/bwa/index/main.nf
@@ -22,8 +22,8 @@ process BWA_INDEX {
     path fasta
 
     output:
-    path "bwa"          , emit: index
-    path "*.version.txt", emit: version
+    tuple val("bwa/$fasta.baseName"), path("bwa"), emit: index
+    path "*.version.txt"                         , emit: version
 
     script:
     def software = getSoftwareName(task.process)

diff --git a/modules/nf-core/software/bwa/mem/main.nf b/modules/nf-core/software/bwa/mem/main.nf
@@ -20,7 +20,7 @@ process BWA_MEM {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    tuple val(index_name), path(index)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -31,13 +31,11 @@ process BWA_MEM {
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa mem \\
         $options.args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        $index_name \\
         $reads \\
         | samtools $options.args2 --threads $task.cpus -o ${prefix}.bam -
 

diff --git a/modules/nf-core/software/bwamem2/index/main.nf b/modules/nf-core/software/bwamem2/index/main.nf
@@ -22,14 +22,14 @@ process BWAMEM2_INDEX {
     path fasta
 
     output:
-    path "bwamem2"      , emit: index
-    path "*.version.txt", emit: version
+    tuple val("bwamem2/$fasta.baseName"), path("bwamem2"), emit: index
+    path "*.version.txt"                                 , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
     mkdir bwamem2
-    bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
+    bwa-mem2 index $options.args $fasta -p bwamem2/${fasta.baseName}
     echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
     """
 }
diff --git a/modules/nf-core/software/bwamem2/mem/main.nf b/modules/nf-core/software/bwamem2/mem/main.nf
@@ -20,7 +20,7 @@ process BWAMEM2_MEM {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    tuple val(index_name), path(index)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -31,13 +31,11 @@ process BWAMEM2_MEM {
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa-mem2 mem \\
         $options.args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        $index_name \\
         $reads \\
         | samtools $options.args2 -@ $task.cpus -o ${prefix}.bam -